Sequence
atgc intronic sequence ATGC exonic sequencegtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G10950.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os11g07910.1 (Oryza sativa), 3'ss of exon 7
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctct-agcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
| ||| | | | | | | || ||| | | || | ||| || | | | ||| |||| || | || | | || | |||||| | ||||| ||||| |||||||||||||| ||||| ||||||||||| ||| |||| | |||| | || | || || || | ||||||| |
------------------------------------------------gtgactggacgaattatttgaatattcatagcaaatcattttgcattattttcatcta-atctcttgatagtt-ttgttaacttatatttttcttttatcagGAAAGAGATGTTAGTGAGGAATCTGGTTGGAAGCTTGTCCATGGAGATGTTTTCCGGCCTCCTCGTAGCTTGGTGTTTCTTTCTGCTTTTGTTGGTATTG
upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 3'ss of exon 7
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggca-cagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
| | | ||| | | | | | | | |||| |||||||| | || | | | || | | |||||| | ||||| |||||||||||||| ||||| ||||| ||||| ||||| ||| |||| | | ||| | | ||| || ||||| | |||||| |
-------------------------------------------------------------gtgattgactatctatattcaaataatgtacaaattctgttatgc---gcttcatacatcctcttgctgacatttttattcaatatcagGAAAGAGATGTCAGTGAAGAATCTGGATGGAAGCTTGTCCATGGGGATGTTTTCCGGCCTCCTCGCAGTTTGGCTCTTCTTTCAGCCCTTGTTGGTGTTG
upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G165631_T01 (Zea mays), 3'ss of exon 6
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcac-agGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
| || || | | || | | ||| | | || | | | | | || |||| |||| || | | | | || || || |||| | ||| | | | ||||||| ||||| | |||||||||||| ||||| ||||| ||||| ||||| ||| |||| | | | ||||||||| || ||||| | ||||||| |
--------------------gtgagtttctatatatatgatcatggtgtta--ttccagtagcgttttaatatttatgcagg--ttctgattttaatt---agtttata--cttgtatcctttgctgatata--cattagtttgtattagGAACGAGATGTCAATGAAGAATCTGGATGGAAGCTTGTACATGGTGATGTTTTCCGGCCTCCTTGCAATCTAGTTCTTCTTTCAGCTCTTGTTGGTATTG
upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 7
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattg-atgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
|||| | || || | ||| | ||| | || | ||| | |||| |||| | | | | | | || ||||| | | || | | || | || |||| | | |||||| | ||||| |||||||||||||| ||||||||||||||||| ||||| || |||| | | ||| | ||| | || ||||| | ||||||||||
gtgaggctttcttgatgtttgtctgttactatt------attactatttt-----ttaaaatttatgtgtggaacata-gattctactttcctggaaaattcattgtggttctgattgtcaattcttgttcaacccccatacatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTATTGTTGGTACAG
upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G20100.1 (Glycine max), 3'ss of exon 7
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattga-tgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
|| | | || || | ||| | ||| | || | | ||| ||||| || | | | | | | | || || | | | || | | || | || |||| | | | |||||| | ||||| |||||||||||||| ||||||||||||||||| ||||| || |||| | | ||| | ||| | || ||||| || ||||||||||
gttaggctttcttgatgtttgtctgttactattattattattattttt---------aaaatttatgtgtggaacatagattctgttttcctggaaagttcattgtg-gttctgattgtcaattcttgttcaacccccaaatatttccagGAAAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAGTTTGGTTATTCTTTCAGCTGTTGTTGGTACAG
upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA05G30210.1 (Glycine max), 3'ss of exon 7
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
|||||| || | |||||||| | | |||| ||| ||| | ||| || ||| | | | | || | | | | | | ||| | | ||||||| | ||| |||||| | ||||| |||||||||||||| ||||||||||||||||| ||||| || |||| | | | ||||| | || ||||| || ||||| || |
gtgatggtttcgtgacttttatct-taattatttgtggaat-------------atgaatcctttcttac--tagataaagcattgtggttctaattgttgaatatt--------tggtcatttct----------tccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGGCCTCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACTG
upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G13370.1 (Glycine max), 3'ss of exon 7
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
|||||| || | |||||||| | | || | ||| ||| | | || ||| ||| | | | | | |||||| || | | | ||||||| | ||| |||||| | ||||| |||||||||||||| ||||||||||||||||| ||||| || | || | | | ||||| | || ||||| || ||||| ||||
gtgatggtttcatgacttttatctttaataatttgtggaata--------------tgaacctttct---------tcctagagaaatcattgtggttctaattgtcgaatatt-tggtcatttct----------tccatgcttacagGAGAGAGATGTTAGTGAAGAATCTGGCTGGAAACTTGTGCATGGTGATGTTTTTCGACCGCCTCGCAACTTAGTTATTCTTTCAGCTGTTGTTGGCACAG
upper sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 7
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
||| | |||| || | || | | |||| | | | | | | | || | || || || | || | || | | ||||| |||||| |||||||||||||||| ||||| ||||||||||| ||||| ||||| || || | | | | | | ||| | | ||||| || ||||| || |
------------------------------------gtaatgctattttaagttcttgactgtgtctatgtttttttttttttttaatatatatagtccttaagtgaaaattatgtatcttattttccactatatattgt------cagGAAAGGGATGTAAGTGAAGAGTCTGGCTGGAAACTTGTCCATGGGGATGTTTTTCGGTCTCCTCGCAATATGGTTTTATTTTCAGCTGTTGTTGGCACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
tattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgtttcctcaacttttatttgtcattagttgcacaattgtttttttagctgttaatactctctagcagtctgtccaacacttctttctttacttctaaatgcaaggcttcatagccatttctgacgtgagtattgatgggcacagGAACGGGATGTAAGTGAAGAATCTGGTTGGAAACTTGTGCATGGAGATGTGTTCAGGCCAGCAAGTAGTCTAGTTCTGCTCTCAGCGGTAGTTGGTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG