Sequence
atgc intronic sequence ATGC exonic sequencegtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 3'ss of exon 6
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactga--------aagtattattaatct----------tttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
||||| ||||||| | | | || ||| | | || | | || || ||||| | |||| |||||||| | | | | | || | || |||| || | || | |||| || || |||||| ||| |||||||| ||| ||||||||||| |||||||||| ||| ||| || ||| |||||||| ||| |||||||||||||||||||||| ||||
gtattgaaatcccagatctgtgatgtttttctacagatataaatattcatcggaagctaaaatttctgaggcgataaagtaaagaagtcactattgtttttgttttgctaacataatgtaattgacattacactggcaaatgatttcagGGTGTACTAACCTATGGAAAAATTGGTGAATGGAGATTTGACAAGAGAGCATACCAAGACAGGCCACCGCCACGAAATCTTACATTGCCCCCTCCAGGAG
upper sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G26610.1 (Glycine max), 3'ss of exon 7
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
| | || ||| | | || | ||| | | | | | | || ||| | | |||||| | | ||| | | | | ||| || | | |||||||| |||| ||||| ||||||||||||||| ||||||||||||| || | | | || ||||||| ||| | | ||||||| || || |
-------------------act--ttgctttagcagatatacttttattggaacactgtagcttcctg---tcatctattgtatatttc----tcctagttgtctca---atagtgtttcatgattctcagGGTGAATTGACTTATGGCAAAGTTGGTGAATGGAGATTTGACAAAAGGTCGCATCTACGAGGACCTCCACCAAAAAACTTGCCCCTGCCCCCACCAGGGG
upper sequence: GRMZM2G035595_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv13s0084g00830.t01 (Vitis vinifera), 3'ss of exon 6
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
| |||| | | || || ||| | ||| | | | || || ||| ||| ||| || | | ||| | | | ||||| || || || || ||||||| ||||| ||||| ||| |||| || |||||||||||||| ||||||| || | | | || || || ||||| ||| | ||||| ||||| || |
----------ctattactggctcttatcatcgttatgtttgggtatc--cctaagttcg----cattttgtg------gtattggttctgtggtta-------tctgttcaaagt-ttcttgatattc-agGGTGAGCTGACATATGGGAAAATTGGAGAGTGGCGATTTGACAAGAGATCATACCTACGTGGACCTCCTCCTAGAAACCTTTCCTTGCCGCCTCCAGGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
tattaat putative branch site (score: 2)
tctttt CT-rich tract
ttattttactgaaagt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattagaatcccaaactgattaatttcttcaatatatctggtttccatacgaaatttaaaaatattgagtgcataaagtagatattttattgttcctgttattttactgaaagtattattaatcttttagGGTGAACTGACCTATGGTAAAGTTGGTGAATGGCGATTTGACAAAAGATCATTCCCAGATAGGCCACCACCAAGAAATCTTACATTGCCCCCTCCTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA