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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA

Basic information

species Zea mays
transcript GRMZM2G059381_T01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 18
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
      || | |  | | | |   || |    ||| || | |   | ||   |   | |  ||    |  ||  |     |||| | | |    |   ||||| |||||||| || ||||| || ||||||||||| ||||| ||||||||||| || ||||| ||| | || || |  ||| || | || || || || 
------gttttataaatcaaaacattctt--gttatttctttc--tttgcggaagaaaaagttgaaatgtttgttaaaacttcaatgtgc---atgacagGAAGAAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATT

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 18
gtgttggtctgactagttacatttttgtgtaattaattgtgttgg-tctgactagttacatttttgtgtaattaattgtttttcacttttctgggttga-agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
   ||| |   |  ||  || || |   |      |   ||     | | | |  | | ||||| || |  |||       || |           ||| |||||||||||||| |||||| | || || || ||||| ||||| |||||||| ||||||||||| ||||| |||||||| ||  || | ||||| ||||| 
-aattgcttacaaaagaaactttgtgaagagcaggaacatgccaactttaagttatgaaattttagtctc-ttagcgaaaattgatggccaacttatgacagGAAAAAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATC

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
--------------------------------------------------------------------------------------------gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaatt-gtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                                                             | ||||||     | ||   | ||  | ||||  | | |  |    |   |  |||| | |   | |  |   || || ||  |  ||  |   |   ||||| ||||||||||| ||||| || |||||||| ||||||||||||||||| ||||||||||| |||||||| ||||| ||  |||| || |||||| ||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
-gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttt-tcacttttc-tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
 ||  ||    ||  | ||    ||||   |  | |    ||||      | |||| |  || |  | |   |  |||||   ||| |  ||     ||| ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    |||||  | || || |  |||
tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcac--aagtagt-atgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 3'ss of exon 21
------------------------------------------------------------------------------gtgttggtctgacta-gttacatttttgtgtaattaattgtgttggtctgactagttacatttttg----tgtaattaattgtttttcacttttctgg--gttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                                              ||       ||| || |||  | | || |    ||    |  |   ||  |||    | ||||  |    | | || | ||||   |   ||   |||   ||| || || ||||| || |||||||| ||||| ||||| ||||| || || |||||||||||||| |||||        |   ||||||||| || |||||||| 
gtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaag-atcaatccaactttgaatatttcaggagctttcatgagttgtacgttctttccttggttattgcagAAAGAAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATT

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 3'ss of exon 20
--gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
  || ||  |||     |  || | |   |  ||  |||| | | |   || |   |   ||  |  |||  |   |||| |       |    |  || ||||| ||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||| ||| | || || ||  ||
aagttttattcttctctgaaac-tgtaactagaaaaaattatctggaagtggcagttcttatgctcatgtt-tgttttgtatcctttaatcactgtctgcagGAAGAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTA

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ37488 (Selaginella moellendorffii), 3'ss of exon 19
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacat-ttttgtgtaatt-aattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                     || || |  ||||||| |||  ||| |  || || |   |   |   ||||||||||||||||| ||| | || || || ||||||||||| ||||||||||||||||||||||||   ||  |||||||| ||||||| || ||  | 
-----------------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcattttttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

upper sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ33980 (Selaginella moellendorffii), 3'ss of exon 19
gtgttggtctgactagttacatttttgtgtaattaattgtgttggtctgactagttacat-ttttgtgtaatt-aattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                                                     || || |  ||||||| |||  ||| |  || || |   |   |   ||||||||||||||||| ||| | || || || ||||||||||| ||||||||||||||||||||||||  |||  |||||||| ||||||| || ||  | 
-----------------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcattttttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

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|33090935|gb|CF050929.1|CF050929
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|87153602|gb|DY398391.1|DY398391
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|19350747|gb|BM895279.1|BM895279
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|60395514|gb|DN228384.1|DN228384
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|58030032|gb|CX725459.1|CX725459
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|93283329|gb|EB675593.1|EB675593
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|32847207|gb|CD986888.1|CD986888
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
EST: gi|211308069|gb|FL216534.1|FL216534
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAA

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: 46

AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 25

AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

AAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAGgtaaagctga ... tgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgactagttacatttttgtgtaattaattgtttttcacttttctgggttgaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTCATTGCTCAATGCTTTATA
                       aattaat  putative branch site (score: 211)
                             ttgtttttcacttttc  CT-rich tract
         ttacatttttgtgtaa  TA-rich tract