Sequence
atgc intronic sequence ATGC exonic sequencegtatgattcaacatctttctggaactaaatccatcactgctactttcagatgccaccaaaggaaccaaaaaaatccacttagactgcgtctcctcatggatgactagaagaaccgcacaattgtacaaaatccatattaactggcttgaactcttttctcatgacaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAAAAACCTGAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G12770.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g36180.1 (Oryza sativa), 3'ss of exon 7
gtatgattcaacatctttctggaactaaatccatcactgctactttcagatgccaccaaaggaaccaaaaaaatccacttagactgcgtctcctcatggatgactagaagaaccgcacaattgtacaaaatccatattaactggcttgaactcttttctcatgacaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAAAAACCTGAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA-
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-----------------------------------------------------------aagtgccggga-----cttttaaagagt-tctattttctagtgtttcccattacatccttttggtataaacttta-attaa--------acctcctctatgtttgcacaaaacagGAGGCATGGAACAAATTCAACTCAGAGGAACTCTTCT-AAACGGCCTGCGCAAATGAAACATATTGCTCACCAATCTTCACCTGCATGAGGCAATCGGGGT
upper sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os01g25320.1 (Oryza sativa), 3'ss of exon 7
gtatgattcaacatctttctggaactaaatccatcactgctactttcagatgccaccaaaggaaccaaaaaaatccacttagactgcgtctcctcatggatgactagaagaaccgcacaattgtacaaaatc-catattaactggcttgaactcttttctcatg-acaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAA---AAACCTGAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA-
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---------------------------------------------------------------------------cctgtgtcctactgtccttcattggctagttgattaatgaca-acttatgagccataatgttctattacacttctcttatattctattgtggaataaacagGAAGCATGGAACAAATTCAACTCGGAAGAACTCTTCTAACACTTAATCGTTTGTCAATCCCTGAGCCACTGAGGTACTAGG----AAGGAAACAAATGACATAC
upper sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os11g43950.1 (Oryza sativa), 3'ss of exon 7
gtatgattcaacatctttctggaactaaatccatcactgctactttcagatgccaccaaaggaaccaaaaaaatccacttagactgcgtctcctcatggatgactagaagaaccgcacaattgtacaaaatccatattaactggcttgaactcttttctcatgacaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAAAAACC-TGAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA-
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-------------------------------------------------------------------cattgtttctcttg---ctcatcatgctattgctgtttataagtcttata---ttttattagatgtctgccg-ttcacttatcttccaccgcatttgcataaaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTTTAAACCATCCACCATATGA-ATGGATATAAATGTTCAGCCTAACTATACC-CACATGAAGAACTGG
upper sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G158872_T01 (Zea mays), 3'ss of exon 7
gtatgattcaacatctttctggaactaaatccatcactgctactttcagatgccaccaaaggaaccaaaaaaatccacttagactgcgtctcctcatggatgactagaagaaccgcacaattgtacaaaatccatattaactggcttgaactcttttctcatgacaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAAAAACCT--GAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA
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------------------------------------------------------------------------tttgaactgaaacgagacaaataaaaaagaactgggggagtatctgacaccgttacgacttacgtttataag--taaaatattgcaacttctgtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtacaaaatccatattaactggcttgaactcttttctcatgacaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAAAAACCTGAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA
tattaac putative branch site (score: 1)
aaaatccatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattcaacatctttctggaactaaatccatcactgctactttcagatgccaccaaaggaaccaaaaaaatccacttagactgcgtctcctcatggatgactagaagaaccgcacaattgtacaaaatccatattaactggcttgaactcttttctcatgacaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAAAAACCTGAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC