Sequence
atgc intronic sequence ATGC exonic sequencegttagtcaaaatcatggtctttgtgatctctgacatgagcttggtcagtttaggctgcacatatgttgaaatcctttctgattaattgcgctgaaagtttgtaacttttctctgcaccattcttgtttgtggatttcattaatgtatcttggttttatgcagCTTCAAGAACTAGCTACTCAGCTAACTGATCTATGGAATCTGATGGATACTTCTGATGAGGAAAGGGAGCTTTTTGACCATGTTACCTCTAACATTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26760.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G46450.3 (Glycine max), 3'ss of exon 5
gttagtcaaaatcatggtctttgtgatctctgacatgagcttggtcagtttaggctgcacatatgttgaaatcctttctgattaattgcgctgaaagtttgta-acttttctctgcaccattcttgtt----tgtggatttcattaatgtatcttgg---ttttatgcagCTTCAAGAACTAGCTACTCAGCTAACTGATCTATGGAATCTGATGGATACTTCTGATGAGGAAAGGGAGCTTTTTGACCATGTTACCTCTAACATTTCAG
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----------------------------------------------------------------------ccccagagtgatattacctacaaaatgtttttgcattcatttctgcttgacttttaatctaataccattttctttactttgacctggatatttcatgcagCTCCAAGAATTAGCTTCTCAGTTAATTGATCTTTGGAATCTAATGGATACTCATCCCGAGGAAAGGAGACTATTTGACCATGTTACCTGTAATATGTCAG
upper sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G02180.4 (Glycine max), 3'ss of exon 5
gttagtcaaaatcatggtctttgtgatctctgacatgagcttggtcagtttaggctgcacatatgttgaaatcctttctgattaattgcgctgaaagtttgtaacttttctctgcaccattcttgtttgtggatttcattaatgtatcttgg---ttttatgcagCTTCAAGAACTAGCTACTCAGCTAACTGATCTATGGAATCTGATGGATACTTCTGATGAGGAAAGGGAGCTTTTTGACCATGTTACCTCTAACATTTCAG
| | ||| || | | ||| || || | || | |||| | | ||| | |||| ||| | | | ||| | | |||||||| |||||| ||||| ||||| | | |||||| |||||||| ||||||||| | ||||||||| || |||||||||||||||| ||| || ||||
----------------------------------------------------------tcccagagtgatattacct---actaaatgttttgca--ttcattacttgcttgacttttaatctaat--accattttctttactttgacatggatatatcatgcagCTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACTCATCCCGAGGAAAGGAGACTATTTGACCATGTTACCTGTAATATGTCAG
upper sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 4
gttagtcaaaatcatggtctttgtgatctctgacatgagcttggtcagtttaggctgcacatatgttgaaatcctttctgattaattgcgctgaaagtttgtaacttttctctgcaccattcttgtttgtggatttcattaatgtatcttggttttatgcagCTTCAAGAACTAGCTACTCAGCTAACTGATCTATGGAATCTGATGGATACTTCTGATGAGGAAAGGGAGCTTTTTGACCATGTTACCTCTAACATTTCAG
|| | | | | || || | || ||||| | | | | | | || ||| || |||| ||| | | ||||||||||| |||| |||||||||| |||||| ||||||||||||||||| | || ||||| || | ||||| |||||||||| |||||| || |
------------------------------------------------------------tcatatgagatctatatatgttttttcgctttgaaaatcactgcacctgttggttgctacgacaaaatgaattattctttgatgtgtctc--ctctccacagCTTCAAGAGTTAGCCACTCAGCTAATTGATCTGTGGAATCTGATGGATACCCCAGAGGAGGAGCGGAGTTTGTTTGATCATGTTACCTGTAACATATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctctgcaccattcttgtttgtggatttcattaatgtatcttggttttatgcagCTTCAAGAACTAGCTACTCAGCTAACTGATCTATGGAATCTGATGGATACTTCTGATGAGGAAAGGGAGCTTTTTGACCATGTTACCTCTAACATTTCAG
cattaat putative branch site (score: 3)
atttcattaatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtcaaaatcatggtctttgtgatctctgacatgagcttggtcagtttaggctgcacatatgttgaaatcctttctgattaattgcgctgaaagtttgtaacttttctctgcaccattcttgtttgtggatttcattaatgtatcttggttttatgcagCTTCAAGAACTAGCTACTCAGCTAACTGATCTATGGAATCTGATGGATACTTCTGATGAGGAAAGGGAGCTTTTTGACCATGTTACCTCTAACATTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT