Sequence
atgc intronic sequence ATGC exonic sequencegtgatgggttataattcctttggcaacttttcttataattgaatttacaaaagttgtcttaaatagataccagtgttgtgagcatatcacccccgtatgatactgtttattgacattgtgattgtattgacactgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53390.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G36480.2 (Glycine max), 3'ss of exon 3
----------------------------------gtgatgggttataattcctttggcaacttttcttataattgaa----tttacaaaagttgtcttaaatagataccagtgttgtg--agcatatca--cccccgtatgatactgttta-----ttgacattgtgattgtat-----tgacactg-----acagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
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gttagtcttgtttggttctagtcaattaattaatgaaatcggcatttatggatccgtttcctttttccctagttcacctctttctctagagcttatataaaataatatgtatcttactctagcttgtgattcttctgtttttggttaattaatactttgagaatacaatttcacaatcataactctgctttaacagCATGGATGGAAAATATATTTTGACGGGAGGGGAAGATGATTTAGTTCAAGTTTGGAGCATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACATAAC
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G05890.1 (Glycine max), 3'ss of exon 9
gtgatgggttataattcctttggcaacttttcttataattgaattt-acaaaagttgtcttaaatagataccagtgttgtgagcatatcacccccgtatgatactgtttattgacattgtgattgtattgacactgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
||| | || || | | | | | || | ||| | || | | || | | || | || ||| ||| || | ||| ||||||||||| || |||||||| ||||| || ||||||||||||||||| ||||||||||| ||||| || |||||||| |||||||||||||| ||
------------------------------------aatagtgcttgacttactctattgttactatggttctttgtcttttctttaattcatacttaaaaaa---ttcaatgccataatgaaaagtctgctg-taccagCATGGATGGAAAATATATTTTGACGGGAGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGACACAAC
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G33740.1 (Glycine max), 3'ss of exon 8
gtgatgggttataattcctttggcaacttttcttataattgaatttacaaaagttgtcttaaatagataccagtgttgtgagcatatcacccccgtatgatactgt-ttattgacattgtgattgtattgacactgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
||| || | || | | |||| | | || | | |||| ||| ||| ||| | ||||| ||| | || || | | | || ||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||| ||||| ||||| || |||||||| ||||| |||||||||||
------------------------------------ttttgggttaattaatact-ttgagaatacaatttcataatgatacaacatcaaacccttatcccactttgttatt--cataataataactctg-ctttaatagCATGGATGGAAAATATATTTTGACGGGAGGGGAAGATGATTTAGTTCAAGTTTGGAGCATGGAAGATCGCAAGGTTGTGGCATGGGGCGAGGGACATAAC
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G20240.1 (Glycine max), 3'ss of exon 9
------------------------------------------gtgatgggttataattcctttggcaacttttct--tataatt---gaatttacaaaa----gttgtcttaaatagataccagtgttgtgagc-atatcacccccgtatgatactgtttattgacattgtgattgta-----ttgacactgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
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gtgaggcatatttggttttggtcaatcaattaatggatctttggattaatctcctatttcctcagttcctttcttactctagctcaagagcttctaaaataacagtgcttgactttgctgttactgtggttggttgtctctcctttaattcatacttcaaaaacacaatgctataatgaaaagtctgttttaacagCATGGATGGAAAGTATATTTTGACGGGGGGAGAGGATGATTTAGTTCAAGTTTGGAGTATGGAAGATCGCAAGGTTGTGGCATGGGGTGAGGGGCACAAC
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0040g01960.t01 (Vitis vinifera), 3'ss of exon 8
gtgatgggttataattcctttggcaacttttcttataattgaatttacaaaagttgtcttaaatagataccagtgttgtgagcat-atcacccccgtatgatactgtttattgacattgtgattgtattgacactga-cagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
| | | | | || | || | | | | | | || || || ||| | | | | | | || | | | ||| |||| ||| |||||||||| || ||||||||||||||||| |||||| |||||||||| ||||||||||| |||||||| |||||||| |||||||||||||| ||
-----------------------------------------acatgatatcatttcttctagttctttttccttttgtaaaatattattactccctttgaaaagagagtggtataatagacaacaaaatgatgctgaacagCGTGGATGGAAAATATATTTTGACTGGAGGTGAGGATGATCTAGTTCAAGTTTGGAGTATGGAAGATCGGAAGGTTGTGGCATGGGGTGAGGGACACAAC
upper sequence: AT3G53390.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S193_64V6.1 (Physcomitrella patens), 3'ss of exon 8
gtgatgggttataattcctttggcaacttttcttataattgaatttacaaaagttgtcttaaata-gataccagtgttgtgagcatatcacccccgta--tgatactgtttattgaca-ttgtgattgtattgac-actgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
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--------------------------------------------tcatcattactctcttgaatgcggctgtagtgtactaaaatagaaaccttgggaagtgaaaagttgtcttgacaatcacaatggggttggctattggtagTCCGGATGGGAAGTACATATTGACAGGTGGAGAAGACGATCTTGTACAAGTTTGGAGTATGGAGGATCAAGCCGTCGTTGCTTGGGGGGTGGGGCATAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcacccccgtatgatactgtttattgacattgtgattgtattgacactgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
tattgac putative branch site (score: 2)
tgtttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatgggttataattcctttggcaacttttcttataattgaatttacaaaagttgtcttaaatagataccagtgttgtgagcatatcacccccgtatgatactgtttattgacattgtgattgtattgacactgacagTATGGATGGAAAGTACATTTTGACTGGAGGTGAAGATGATTTAGTTCAAGTGTGGAGTATGGAGGATCGGAAAGTTGTGGCGTGGGGTGAGGGACATAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT