Sequence
atgc intronic sequence ATGC exonic sequence...caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 1
-caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgata-tatgattctatccatatgccacttgcagcagttctgtag-
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atgatttagttgaagaaatgcgtcgtcgtcgagttgtatagcaaca--atgatcaggcactactacttgttaaagtattaactctctgcagctcttctgtagGAAATGGCTGACGGTGAGGACATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g01600.1 (Oryza sativa), 3'ss of exon 1
----caaatccactgttccttttc--aaccacatagt----gaaccaaaacactctcatcactgagcgata-tatgattctatccatatgccacttgcagcagttctgtag-
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agtactcatcaatgatttagttgaagaaatgcgtcgtcgtcgagttgtatagcaacaatgatcaggcactactacttgttaaagtattaactctctgcagCTCTTCTGTAGGAAATGGCTGACGGTGAGGACATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G15520.1 (Glycine max), 3'ss of exon 1
-----------caaatccactgttccttttcaaccacatagtgaaccaaaaca-ctctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAA-TGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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agagtttgaagtaaaccctcaaagtctgta-aatggctgggttctgtagattgtctattcaaacttggtggtac-tga--caatttattgtatgcgtactgtagTTTGGTAAAAAATGGCTGATGCTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 1
----caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatg---attctatccatatgcc----acttgcagcagttctgtagAA-ATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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tatagaaaataaacgtaatcttcaaagtctgtaagtggctgggttctgcagattgtctattcaaacttgttaatactggcaatttgttctatgcatacagTAGTTTGGTAAAAGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G39380.1 (Glycine max), 3'ss of exon 1
-caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatg---attctatccatatgcc----acttgcagcagttctgtagAA-ATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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agaaaataaacgtaatcttcaaagtctgtaagtggctgggttctgcagattgtctattcaaacttgttaatactggcaatttgttctatgcatacagtagTTTGGTAAAAGATGGCTGATGCTGAGGATATTCAACCCCTTGTCTGTGACAATGGAACTGGAATGGTGAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 1
------caaatccac-tgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatc-catatgccacttgcagcagttctgtagAA-ATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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cttcgttggctgtaaatgtcctggtttcacgggttgtccatacaatacaattttgttacttactgacactttacttcatggcaccctatgctttctgtagGTTTGTAAAAGATGGCAGATGCCGAGGATATTCAACCCCTTGTTTGCGACAATGGAACTGGAATGGTCAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 1
-------------caaatcc---actgttccttt-tcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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tctctagtagtttcaaacttttgatcgttgcttcatcttttctttggttttgttttttatttcctttcctgaacaacttatc-tcccgttc--------tctgctacagGTTTTAAAAAATGGCTGATGCTGAGGACATTCAACCTCTTGTTGTTGATAATGGAACTGGAATGGTCAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 1
caaatccactgttccttttc--aaccacatagtgaaccaaaacactctcatcac-tgagcgatatatgattctatccatatgccacttgcagcagttctgt--agAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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aataaacgctgctaatcttcgaaactaagttgtgatctgattcgtgtttacttcatgagct-tatccaattcatttcggtttcattttactttttttttagTGAAAAATGGCCGATGGTGAGGATATTCAGCCACTTGTCTGTGACAATGGAACTGGAATGGTGAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: PP1S372_38V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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atcagtctatcgaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttagGTGTTGCAAAGTGGTTGAGCAGGTCCAAACTA-AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 2
-------------caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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cagtatggagggcgttctgtactgtcctgattgcgagacatgttttacgacgaaaat-ttactgctccttagaactaaaatcttctgaaatggttgggcagGTCGGTATTAAGAAATGGCTGACGGTGAGGAAGTACAGCCCTTGGTGTGCGACAATGGAACTGGAATGGTCAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: PP1S372_38V6.4 (Physcomitrella patens), 3'ss of exon 1
-------------caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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ccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttaggtgttgcaaagtggttgagcagGTCCAAACTA-AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG
upper sequence: GRMZM2G067985_T09 (Zea mays), 3'ss of exon 1
lower sequence: PP1S372_38V6.3 (Physcomitrella patens), 3'ss of exon 1
------------------------caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
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gaatccacctaccaggactaggatcagttgtaatgttcgcctcccttgggataattcatgaaagaagacaaattgtatttcgtgcttaggtgttgcaaagTGGTTGAGCAGGTCCAAACTA-AACCATGGCTGATGGTGAGGAAGTCCAGCCTTTGGTGTGCGACAATGGCTCTGGAATGGTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
atatatgattctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaatccactgttccttttcaaccacatagtgaaccaaaacactctcatcactgagcgatatatgattctatccatatgccacttgcagcagttctgtagAAATGGCTGATGGTGAGGACATCCAGCCTCTTGTCTGCGACAATGGCACTGGAATGGTCAAG
- - -ccactgt
- - - - - - - - - -caaccac
- - - - - - - - - - - - - - - tgaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcagc