ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA

Basic information

species	Zea mays
transcript	GRMZM5G852968_T02
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g36450.2 (Oryza sativa), 3'ss of exon 6

gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA----
|||| | |||||||||||  | ||   || ||    |||     || ||   |      |||    | |     || |  | ||| ||   ||||||||   ||||| |||| |||||| |||||||||| ||||| || ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||    
gtgacaattcttcatcttgag-ttaaattaataatggtt-----gatgagccta-----catcatctgaagacaagat--tcatgtat---caacatgt---tgctttcagacagTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCATGCT

upper sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 3'ss of exon 6

gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA
|||| | |||||||||||  | ||   || ||    |||     || ||   |      |||    | |     || |  | ||| ||   ||||||||   ||||| |||| |||||| |||||||||| ||||| || ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||||||
gtgacaattcttcatcttgag-ttaaattaataatggtt-----gatgagccta-----catcatctgaagacaagat--tcatgtat---caacatgt---tgctttcagACAGTATTACAAACTGGGCGGATGTAGTAATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGGAAAGTTGCTACTCCTGAGCAAGCTCAGGAAGTTCA

upper sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G34300.1 (Glycine max), 3'ss of exon 6

------gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgat-gcatgcgcaacat-----gtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA
      |  |  | | ||  |  ||  ||   ||| | |  | || |          |||| |   |   | |      |   || |||| || |||  |||||     || ||||  ||||||     || | |  |||| | |  |||| ||||||||||| ||||| ||||| |||||||| || ||||| || |||||  | ||||| |||||||| ||
gtaggtgcaagctatatttctaatataatccatttaaagtccattttct--------ttggaaaaaacaaactggagagggtttgctgattgcttgcataacatccatcgtgtctgtatgcagACGCAGTTGCTAGTTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCCATTGGAACGGGCAAAGTGGCCACTCCCCAACAAGCTCAGGAAGTACA

upper sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G36990.2 (Glycine max), 3'ss of exon 6

---gtgaaatttcttcatcttagg-attttttttatgg---gcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgat-gcat-gcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA
   ||| || || |   |||||   | |   ||||      |  ||||   ||   ||  |  |   |  |     | ||  |  |||||| ||||  |      ||    |  || |||||    || | | ||||| | |  |||| ||||||||||| ||||| |||||||||||||| || ||||| || |||||  ||||||| |||||||| ||
gtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgatttagaagaaacaaaaggggaaggatttggtggttgattgcattacatcgtttgccattatttacagATGCAGTTCCTAGCTGGGACAACATTGTTATTGCATATGAACCTGTATGGGCTATTGGAACGGGCAAAGTGGCCACTCCCCAGCAAGCTCAGGAAGTACA

upper sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G06740.1 (Glycine max), 3'ss of exon 6

gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA
          || || | |   |  ||||  |    | |  ||| |||||     | || | ||  ||  |    | |       ||| |   |  |  || |   |||||||    |  |||  ||||   || | || ||||||||||||||||| ||||| |||||||| || ||||| || || || ||||||||||||||||| ||
----------tttatttgaaagtcattttctttttaggtggagaaaagaaaagaagggggagtgggttgccgattgattccataacatcctttatgtccat-tatatgcagATGTAGTGCCAAGTTGGGATAATATAGTTATTGCATATGAGCCTGTATGGGCAATTGGAACTGGCAAAGTGGCCACACCCGAGCAAGCCCAGGAAGTCCA

upper sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G20930.1 (Glycine max), 3'ss of exon 6

gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatg-catgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA
          |||||   |   |  | ||  |    | |  ||| ||||| | ||        |   ||||     || |  ||  ||| |   |  |  || |   |||||||    |  |||  ||||   || | || ||||||||||||||||| ||||| |||||||| || ||||| || || || ||||||||||||||||| ||
----------ttcattagaaagtcatcttctttttaggtggagaaaagaa-taggagcaagaggggatagcagattgtttccataacatcctttatgtccat-tatgtgcagATGCAGTGCCAAGTTGGGATAATATAGTTATTGCATATGAGCCTGTATGGGCAATTGGAACTGGCAAAGTGGCCACACCCGAGCAAGCCCAGGAAGTCCA

upper sequence: GRMZM5G852968_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 3'ss of exon 6

gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgctt---------gcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA
  | || ||||    || | | | | |||     |   | ||  |  |   |  ||     |||    |     |  ||||||  | |  | |||||   |||  ||         ||||||  | |  | |  ||||  ||||| || |||||||||||||| ||||||||||||||||| || ||||| || || ||   ||| || |||||||| ||
--gcaagttctcttgctgatgttctctttctcatggaatgtactgtcgttttgtggtcctcttgtgaaaagagaacttgttgactcttttgtaacatcgctcttgttcaatcatgcgcagATGCTGTACCCAGTTGGGATGATGTAGTTATTGCATATGAGCCGGTTTGGGCTATTGGAACTGGTAAAGTGGCCACACCCCTGCAGGCACAGGAAGTACA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|37381263|gb|CF627507.1|CF627507

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|71757354|gb|DR955291.1|DR955291

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|101387332|gb|EB815682.1|EB815682

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGGCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|71319071|gb|DR796286.1|DR796286

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|149089024|gb|EE178175.2|EE178175

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|13126489|gb|BG317059.1|BG317059

EST:     TTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: TTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|60344413|gb|DN211386.1|DN211386

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|78089192|gb|DV517576.1|DV517576

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|71439314|gb|DR820364.1|DR820364

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|148949372|gb|EC894828.2|EC894828

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|148990724|gb|EE032131.2|EE032131

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|37377574|gb|CF625404.1|CF625404

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|78089319|gb|DV517693.1|DV517693

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|71301510|gb|DR786796.1|DR786796

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|60400606|gb|DN233413.1|DN233413

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|71436978|gb|DR818028.1|DR818028

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|148987083|gb|EE030908.2|EE030908

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCCGATGTTGTGATTGCATATGAGCCTGTTTGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCC-GATGTTGTGATTGCATATGAGCCTGTTTGG

EST: gi|148945255|gb|EC890464.2|EC890464

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|91877369|gb|EB407326.1|EB407326

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|148942891|gb|EC887934.2|EC887934

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|86469699|gb|DY236069.1|DY236069

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|91049452|gb|EB159870.1|EB159870

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|78089320|gb|DV517694.1|DV517694

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|149111298|gb|EE294796.2|EE294796

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|45567946|gb|CK985826.1|CK985826

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|76011527|gb|DT938697.1|DT938697

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|71758305|gb|DR956242.1|DR956242

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

EST: gi|78089191|gb|DV517575.1|DV517575

EST:     AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG
genomic: AGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTTCTGGAAGAGAGGGAAGCAGGGAAAACTTTTGAAGTATGTTTTGAGCAGATGAAGGCTTTTGCAGgtgaaatttc ... ctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 750

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 402

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

aggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA

                     tgttgat  putative branch site (score: 402)
                                            tctgctt  putative PPT
     ttgattta  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaatttcttcatcttaggattttttttatgggcgttctagagaagaagttgggaggcattgatttagcttgaggtgttgatgcatgcgcaacatgtatctgcttgcagATAGTATTTCAAACTGGGCCGATGTTGTGATTGCATATGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAGCAAGCCCAGGAAGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG