Sequence
atgc intronic sequence ATGC exonic sequence...aacaataaacttcctccaataattgggtcctgaaacaagaagcttgaagtcatgatgacatgattgactttttttgcaatttgtttttttcctgagtcagCCTGGTCGTAATATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 5
aacaataaacttcctcca------ataattgggtcctgaaacaagaagcttgaagtcatgatgacatgattgactttttttgcaatttgtttttttcctgagtcagCCTGGTCGTAAT---ATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
| |||| | | || | || || || ||| | || | | || | | || ||| |||| || |||| |||||| ||| |||| ||||||||||| |||||||||||||||||||| || |||||||| || ||||||||||||| ||||| || ||||||||||| |
----ttttgcttcattgataatgcattctactgttctaccacctcgttgttggctttctgtttaaatagt-ggctcactttataattcattgttttgtcaca-cagCCTAGTCCTAATGGCATGTTGGATGACTGGGAGGAGAATTTGGCTATCATAACTGCAAATAGGACAAAAGGTGACGACCTAGTTATTACCCATCTTGGAG---
upper sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 10
----------------------------------aacaataaacttcctccaataattgg-gtcctgaaacaagaagcttgaag-tcatgatgacatgattgacttt----ttttgcaatttgtttttttcctgag---tcagCCTGGTC---GTAATATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
|| ||| | | | | ||| | || ||| | | ||| | || | | |||| || | |||||| || | || |||| ||| | |||| | |||||||||||||||||| ||||| | || |||||||||||||| ||| |||| | || ||||| | || || ||||
gtaatcctaataggataaactaagaagccatgcaaaatatatgcattccagatgtgttgttatgttgcttcaatattttcaaaggttatcagtttctatttgatttggaagctcaaacttttgttattgccttgccatttcagGTTGGATCCGATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAAGTGATGAACTTGTAATTATTCACCTAGGTG---
upper sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
------------------------------aacaataaacttcc--tccaataattgggtc---ctgaaacaagaagcttgaagtc-atgatgacatgattgactttt---tttgcaattt----gtttttttcctgagtcagCCTGGTCGTAAT---ATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
||| | | || | |||| | || || ||| | | |||| || | |||| || | | ||| ||| ||| | |||| ||| ||| ||| | |||||||||||||||||| ||||| | || |||||||||||||| |||||||| | || ||||| | || |||||||
gtaatcctaataagataaactaagaagccatgcaaaatatttgcaatccagatgtattgttacattgcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgttgttgcttttccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG---
upper sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G03580.1 (Glycine max), 3'ss of exon 10
--------------------------------aacaataaacttcctccaataattgggtc---ctgaaacaagaagcttgaag-tcatgatgacatgattgactt-------tttttgcaatttgtttttttcctgagtcagCCTGGTCGTAAT---ATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
| |||| | |||| | || || ||| | | ||| | || | | ||| | || | | |||| ||| | | || ||| ||| ||| | |||||||||||||||||| ||||| | || |||||||||||||| |||| ||| | || ||||| | || |||||||
gtaatcctaataggataaattaagaagccatgcaaaatatatgcaatccagatgtattgttacattgcttcaatagtttcaaaggttattagtttctaattcatttggaagctcaatctttaggtgttgctttgccattttagGTTGGATCCAATGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTTGGTG---
upper sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G41800.1 (Glycine max), 3'ss of exon 7
--------------------------------aacaataaacttcctccaataattgggtcc---tgaaacaagaagcttgaag-tcatgatgacatgattgacttt----ttttgcaatttgttttt--ttcctgagtcagCCTGGTCGTAAT---ATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
| |||| | || | | || | || ||| | | ||| | || | | ||||| || | |||||| || || | ||| ||| || ||| | |||||||||||||||||| ||||| | || |||||||||||||| |||| ||| | || ||||| | || || ||||
gtaatcctaattggataaactaagaagccatgcaaaatatatcaaatcaagacgtattgttccattgcctcaatagtttcaaaggttatcagtttctaattgatttggaagctcaatcttttgttgttgcttttccatccagGTTGGATCCAACGGCATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGATGATGAACTTGTAATTATTCACCTAGGTG---
upper sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 6
--aacaataaacttcctccaataattgggtcctgaaacaagaagcttgaagtcatgatgacatgattgactttttttgcaatttgtttt-----tttcctgagtcagCCTGGTC---GTAATATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
|| | || || || | || | ||| | || | ||| | | | || |||||||| | | || | |||| | |||| | ||||| ||||| ||||||||||| || || ||||| ||||||||||||| ||| | || || || | ||||
tgtgtggtatcagttagttgtgaaatgattcttctaaaattttctttggcattcctttg-cttgagcaagtctattgagtttttgttttaatggcctgcagATATGGGCTGGGGCAAACAGTATGCTAGATGAATGGGAAGAGAATTTGGCCATAATAACTGCTAACAGAACAAAAGATGATGAGCTTGTTATTATTCATC--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagtcatgatgacatgattgactttttttgcaatttgtttttttcctgagtcagCCTGGTCGTAATATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
gattgac putative branch site (score: 3)
tttgtttttttcct putative PPT
tttttttgcaatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacaataaacttcctccaataattgggtcctgaaacaagaagcttgaagtcatgatgacatgattgactttttttgcaatttgtttttttcctgagtcagCCTGGTCGTAATATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT
- caataaa
- - - - - - - - - - - - -ggtcctg
- - - - - - - - - - - - - - - - -aacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - -atgatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgca