Sequence
atgc intronic sequence ATGC exonic sequence...gggggttgttattatttgtttgaaatctgattcaggtcccacattcaaccgggccttatgtgattagttgtaagctgacatgaagatgatgcttttgtagGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G062416_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g17990.1 (Oryza sativa), 3'ss of exon 5
gggggttgttattatttgtttgaaatctgattcaggtcccacattcaaccgggccttatgtgattagttgtaagctgacatgaagatgatgctt-ttgtagGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG
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gcttgcactctttcagaactacaatactgctgtttatgcagccttttggcatatccaa-gtgacaaatgcaaggctgacataaaaatggtgcttattttagGTTCCTCCTACCAGCTTCTTTGATCGCTATCAACGATGTTGCTGCATATTTCTTCGGCTTCTTCTTTGGGAAAACACCCTTAATTAAGCTCTCTCCAAAA
upper sequence: GRMZM2G062416_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 5
-gggggttgttattatttgtttgaaatctgattcaggtcccacattcaaccgggccttatgtgattagttgtaagctgacatgaagatgatgcttttgta--gGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG
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taatgtttgaccattgctattatacgaataagacttgtcctgcactt--ttgcttcttaattgcattgatgttaa-tgtctagtatttggacctattgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATCAAGTTATCTCCAAAG
upper sequence: GRMZM2G062416_T04 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G02210.1 (Glycine max), 3'ss of exon 3
gggggttgttattatttgtttgaaatctgattcaggtcccacattcaaccgggccttatgtgat-tagttgtaagctgacatgaagatgatgcttttgtagGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG
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-tgagcaactgctttggtattgccaaccactatgtttttcatgctttaattgattttattttttatagttacaacctaacatgttaatattatgatgaaagGTTTCTTTTCCCTGCAATCCTCATTGCTATGAATGATGTTGGTGCATATTTCTTCGGTTTCTATTTTGGGAGAACACCTCTGATCAAGCTTTCTCCAAAG
upper sequence: GRMZM2G062416_T04 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 5
--gggggttgttatt-atttgtttgaaatctgattcaggtcccacat-tcaaccgggccttatgtgattagttgtaagctgacatgaagatgatgcttttgtagGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG
|| ||| || | ||| || ||||| | || | | | |||| || ||| || ||||||| | | | || ||||| | || ||||| || | |||| |||||||||| ||||||| ||| ||||||| ||||||||||| | |||||| |||| ||| | ||||||||
aaggactttgccctttacttgattcttgagtgattggattgtcaagtctttggaattctttatttgtttattttc---ctgacat-agtttagtatcaatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACACCTTTGATTAAGTTATCTCCAAAA
upper sequence: GRMZM2G062416_T04 (Zea mays), 3'ss of exon 1
lower sequence: Vv19s0090g01220.t01 (Vitis vinifera), 3'ss of exon 4
----gggggttgttattatttgtttgaaatctg--attcaggtcccacattcaaccgggccttatgtgattagttgtaagctgacatgaagatgatgcttttgtagGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG
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atgagttgtttctcacttcctattaatattgcattattgagtttttttttttggcaactgtttttgttgttggatctaacatggttggatattgatgc------agGTTCCTTCTCCCGGCATCACTTATTGTTATTAATGACATTGCTGCATATTTCTTTGGTTTCTTCTTTGGAAAAACGCCTTTGATCAAACTCTCTCCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaccgggccttatgtgattagttgtaagctgacatgaagatgatgcttttgtagGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG
agctgac putative branch site (score: 3)
tgctttt putative PPT
attagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggggttgttattatttgtttgaaatctgattcaggtcccacattcaaccgggccttatgtgattagttgtaagctgacatgaagatgatgcttttgtagGTTCATCCTCCCAGCTTCGTTAATTGCTATCAATGATGTTGCTGCATATTTCTTTGGGTTCTTCTTTGGGAAAACACCACTGATCAAGCTCTCTCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT