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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatctagccatatgcatgttctgatggtctagtcagtatgtacgatgaaggacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT

Basic information

species Zea mays
transcript GRMZM5G864319_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 8
-ttatctagccatatgcatgttctgatggtctagtcagtatgtacgatgaaggacttttggcaatt-cattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT
    | ||  |  ||   || ||  |  |||||| |||| | ||  | ||  || ||     | || ||||||||| |       |  |   ||   |||||||||  |||||||||||  |||| |||||||| ||||||||||||||||||||||| ||||||||||||||||||||| |||||||||||||||||||||
tgagtttacacgcatagctggtccaacagtctagccagtttatataacgagtgaattacacaattttcattgttctcaaacctgttttt--ttttaatgcagGATGGAATTGAAGAATGCCGAAAACTCTGTGGTGGACATGGTTACCTGAACAGCAGCGGGCTTCCTGAATTGTTTGCTATCTATGTTCCTGCTTGCACTT

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G03800.1 (Glycine max), 3'ss of exon 8
ttatctagccatatgca-tgtt-ctgatg--gtctagtcagtatgtacgatgaag--gacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT
  || ||     ||| | |||| ||| ||  ||   |  | |||      | |    || |||||    |  |||    |||   | ||| |  | | |     ||||||  |||||||||||  | || || ||||| || |||||||||||    |||||||| || ||||| || |||||||| ||||||||||| ||||| |
-catttaaatggatgaagtgtttctgctgtcgttgtgctattatcctttgtaactctgaattttgatgttcaattaagtttaaattaacttcaatttcc-----agGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G14990.1 (Glycine max), 3'ss of exon 7
ttatctagccatatgca-tgtt-ctgatg--gtctagtcagtatgtacgatgaag--gacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT
  || ||     ||| | |||| ||| ||  ||   |  | |||      | |    || |||||    |  |||    |||   | ||| |  | | |     ||||||  |||||||||||  | || || ||||| || |||||||||||    |||||||| || ||||| || |||||||| ||||||||||| ||||| |
-catttaaatggatgaagtgtttctgttgtcgttgtgctattatcctttgtaactctgaattttgatgttcaattaagtttaaattaacttcaatttcc-----agGATGGAATTGAAGAATGCCGTAAACTATGTGGTGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 8
--ttatctagcca---tatgcatgttctgatggtctagtcagtatgtacgatgaaggacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT
  ||| || |      |||   |||| || | ||    | |   | |   |    | ||||||     |   ||    |||   | ||| |  | | |     ||||||  |||||||||||  | || || |||||||| |||||||||||    |||||||| || ||||| || |||||||| ||||||||||| ||||| |
atttaactggatgaagtatttctgttgtggttgtgctattatcctttgtaactctgaactttttatgttcagttaaagttaaattaacttcaatttcc-----agGATGGAATTGAAGAATGCCGTAAACTATGTGGCGGTCATGGTTACCTTTGTAGCAGTGGTCTCCCTGAGTTATTTGCTGTTTATGTTCCTGCCTGCACGT

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT2G35690.1 (Arabidopsis thaliana), 3'ss of exon 7
ttatctagccatatgcatgttctgatggtctagtcagtatgtacga-tgaaggacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT
              | ||| | | |     ||     |    |  | |  |  | | |  || |  |  |||| || | ||      |||    |    ||||||  |||||||||||| | ||| | ||||| |||||||| ||| ||    | |||||||||||||||||||||||||| ||||||||||||||||| |
--------------gtatgctttcaaatcttaacttattaaaataagttgaatattatcagctaaactgtgttttttttgt------tgttggtta-aaagGATGGGATTGAAGAATGTCGTAAGTTATGTGGTGGACATGGATACTTGTGGTGTAGTGGGCTTCCTGAATTGTTTGCTGTATATGTTCCTGCTTGCACAT

upper sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G16760.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------------ttatctagccatatgcatgttctga---tggtctagtcagtatgtacgatgaaggacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT
                                                                ||| | |      ||||||   |   || ||    |   |  |    || |||  | ||   | || |   |||   |   |  | ||   ||  |||||||||| ||||||||||||| | ||| | ||||| |||||||| ||| ||    |||||||||| || ||  |||||||||| ||||||||||| ||||| |
gtaagttccagagctgatcctttatactcactagactagattgattggtttcgtttctctgaggatccaactgctcacatgttggaagtttgttccctccttgacattgtttggaggtgtatttagagttgaaaattcagcttaagggtacta--ttgggtgcagGATGGCATTGAAGAATGTCGTAAGTTATGTGGTGGACATGGATACTTGTGGTGCAGTGGGCTCCCCGAGCTGTTTGCTGTATATGTTCCTGCCTGCACAT

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|33104324|gb|CF064284.1|CF064284
EST:     ACTGCTGGTTTGAAGACTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: ACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
EST: gi|211453990|gb|FL038183.1|FL038183
EST:     CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
EST: gi|211453988|gb|FL038181.1|FL038181
EST:     CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGA-TGTAGAAAGCTCTGTGGCGGACATGGTTA
genomic: CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTA
EST: gi|211453987|gb|FL038180.1|FL038180
EST:     CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
EST: gi|213179269|gb|FM196444.1|FM196444
EST:     CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
EST: gi|33101745|gb|CF061705.1|CF061705
EST:     GTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: GTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
EST: gi|60358249|gb|DN225222.1|DN225222
EST:     CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
EST: gi|211453989|gb|FL038182.1|FL038182
EST:     CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
EST: gi|14204220|gb|BG837897.1|BG837897
EST:     CCTGTACTGCT-GTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: CCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
EST: gi|87153521|gb|DY398310.1|DY398310
EST:     CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCT                         GATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC
genomic: CCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAAC

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), 48 (downstream exon)
Score: 135

GGATGTCACTCAGAAACTGGAAGCTAAAGACTACTCAACACTGCAAGAAGCCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 565

GGATGTCACTCAGAAACTGGAAGCTAAAGACTACTCAACACTGCAAGAAGCCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 528

GGATGTCACTCAGAAACTGGAAGCTAAAGACTACTCAACACTGCAAGAAGCCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 582

GGATGTCACTCAGAAACTGGAAGCTAAAGACTACTCAACACTGCAAGAAGCCCATGCCTGTACTGCTGGTTTGAAGGCTGTGACAACATCTGCAACAGCTgtaagtataa ... ttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaggacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT
                                     ctcctgtcttctgt  CT-rich tract
                aattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatctagccatatgcatgttctgatggtctagtcagtatgtacgatgaaggacttttggcaattcattgttcttatggtgactcctgtcttctgtgcagGATGCCATTGAAGAATGTAGAAAGCTCTGTGGCGGACATGGTTACCTGAACAGCAGTGGGCTTCCTGAATTGTTTGCTGTCTATGTTCCTGCTTGCACTT

- - - - - - -tgcatgt
- - - - - - - - - - -ctgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcctg