Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattcatctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G23920.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 5
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattc-atctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA
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---------------------------------------------tctttgttgggtgcatgcctt------tattacccattttttgaagatctacttttaat---gccttcaccaaaaggatcttactggatggtccttatcattttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCGTTGCTTAAACTAGATGATCCTAATATAG
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 5
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattc-atctttgttgt-gtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA---------------------
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----------------------------------------------tta-attacagtttg-----gtcatttattacccatttcttgaagatctacttttaat---gtcttcaccaaaaggatcttactggatggttctcatcatttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAGGTATTATTCTAAAGTTTTCTT
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G02690.2 (Glycine max), 3'ss of exon 5
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatggg-agataatacaacgaattgtgaattatattaacagatattattcatctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA
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--------------------------------------------------attaacaattaata----aacatttttagcaacataactaaataacacatttcataactgatacaactaacacttgattaatatcctgattttttctttttcagGTTCGTGATTACATTCATGTTCTTGATTTAGCAGATGGGCATATTGCTGCGTTGCGTAAACTGGATGATCCTAAAATAG
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G43540.1 (Glycine max), 3'ss of exon 5
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattc-atctttgttgt-gtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA
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----------------------------------------------tta-attacagtttg-----gtcatttattacccatttcttgaagatctacttttaat---gtcttcaccaaaaggatcttactggatggttctcatcatttttgtcagGTTCGGGATTACATTCATGTTGTTGATTTAGCAGATGGGCACATTGCTGCATTGCTTAAACTAGATGAACCTAATATAG
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaa-attgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattcatctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA
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------------------------------------------------ccttggtaatataggcattatactgcattccagttttccacttttgat-caaaggtttg---atgtcaatgatgtat-tgatgcttacttacc-tattcacatcagGTACGGGATTACATTCATGTTGTGGATTTAGCAGATGGGCACATTGCAGCCTTGCACAAGCTACTCAACTCAGAAATAG
upper sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 5
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattcatctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAG--ATGA-TCTCAAAATCA
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---------------------------------------------------taatttatttgattttcacaatattgtttcggattgaaacttacgaatttatttttaaaatatcgcactctgaatgaa-caactgtgatttggtg-tttcagGTCCGAGATTACATTCATGTCATGGATTTGGCAAGTGGTCATACGAAGGCTCTGGACAAACTCTTCACAACTCCCGACATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acgaattgtgaattatattaacagatattattcatctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA
tattaac putative branch site (score: 1)
tgtttctttc putative PPT
aattatattaacagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgacttatgatgtcttatagacaacaaaccatttgacagatttacattacaatcttaaattgtgatatattatggagtatgggagataatacaacgaattgtgaattatattaacagatattattcatctttgttgtgtttctttcagGTTAGAGATTACATTCATGTCATGGATTTAGCAGATGGACACATAGCTGCTCTGCGTAAGCTAGATGATCTCAAAATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT