Sequence
atgc intronic sequence ATGC exonic sequencegtaagatctaaatctaacctcaagagtttgctgcttcattgttttagcctgatttcttatacgtttttgttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35500.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G33020.1 (Glycine max), 3'ss of exon 2
-gtaagatctaaat---ctaacctca-agagtttgctgcttcattgttttagcctgatttcttatacgtttt------tgttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG
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cgttagttgtgattgctttgacttgacggacacaactacagaagtctataactcagattgcatgttagagtaataaaactttgtgctacgttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
upper sequence: AT4G35500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G09180.1 (Glycine max), 3'ss of exon 2
----------gtaag-atctaaatcta---acctcaagagtttgctgcttc-attgttttagcctgatttcttatacgtttttgttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG
|| | |||||| | | | |||| | | | | ||||||||| | | || || | | || | | | ||| || ||||||||||||| || |||||||||||||| ||||||||||| || |||
tagtagacttgtgattgtctaaagttgttgaacacaagtttctacccttcagattgttttataccagaataataaac-tctgcattgtgttgattt---ttcagGATCACCTTGCCCTAATGATGGAACTCCTTGGAAAGATGCCGCGGAAG
upper sequence: AT4G35500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G21430.1 (Glycine max), 3'ss of exon 2
-gtaagatctaaat---ctaacctcaagagt-ttgctgcttcattgttttagcctgatttcttatacgtttttg------ttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG
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cgttagttgtgattgctttgacttggtgaacacaactacacaagtctataactcagattgcatgttagaataacaaaagtttgtgctacgttggtttcagGATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
upper sequence: AT4G35500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G36260.1 (Glycine max), 3'ss of exon 2
------------gtaagatctaaatct----aacctcaagagtttgctgcttc-attgttttagcctgatttcttatacgtttttgttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG
|| | || || || | | |||| | | | ||||||||| || | | || | || |||| ||| | ||||||||||||| || |||||||||||||| ||||||||||| || |||
tataggtcacttgtgattgcttaaacttgttgaacacaagtctctatccttcagattgttttatactagaataacaaac---tctgcattctg---ttgattccagGATCACCTTGCCCTAATGATGGAACTCCTTGGAAAGATGCCCCGGAAG
upper sequence: AT4G35500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0031g02130.t01 (Vitis vinifera), 3'ss of exon 2
------gtaagatctaaatctaacctcaag----agtttgctgcttcattgttttagcctgatttcttatacg--tttttgttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG
|| || | | || ||||| | || | ||| | ||| | | | ||| | || ||||| ||||| || || |||||||||||||||| |||||||||||||| ||||| || ||||| |||
tgttggttatgaaaaatgcttgacttcaagccatatttcatggaactatttgtataggccaacatattaaaaaaattgttgttgatcggttt-ggtttcagGATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcattgttttagcctgatttcttatacgtttttgttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG
gcctgat putative branch site (score: 4)
atttcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatctaaatctaacctcaagagtttgctgcttcattgttttagcctgatttcttatacgtttttgttatctggttttggatttagGATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG