Sequence
atgc intronic sequence ATGC exonic sequence...tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatctgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57650.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 3
tttgagaaaaaatcattgttttaggttaatacacttctccgcctttttta--------tctgttacatattcatagtactc-ataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
| | | |||| ||| | | || | ||| | || |||| |||| | | | | || |||||| | ||| | || | |||||||| ||||||||||||||||| | ||||| |||||| |||| || | |||||||||||||||| || ||||||
-------tagagcctgtgttaactattacc-ctttcttctgacttctgtagtagatgttctggcacatgatt-tggcattctataaactgtttttgcttacttttgcagGTCATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAGAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G037104_T02 (Zea mays), 3'ss of exon 4
tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttat---ctgttacatattcatagtactc-ataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
||| | | | | | || ||| ||| | | || ||| |||| | | ||| || |||||| | ||| | ||| | ||||| || ||||||||||||||||| | ||||| |||||| ||||||| | |||||||||||||||| || ||||||
--tgaattgatagaacctgtgttaactattaccctttcttctgtagtagatgttctggcacatgatt-tggtattctataaactgt-tttgctcacttttgcagGTTATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAAAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G29600.1 (Glycine max), 3'ss of exon 5
------tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatctgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
| || | | |||| || | || | | | ||||| | || | | | | | | || | ||| | |||||||| ||||||||||||||||| || |||||||| |||||||| |||| ||||||||||||||||||||| |||||
tgtcttatcctgagtagaacattaca--agcatgatttttctacttatgatcccaactagttaccttcaaattgggat-agaggctaagttct---acatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G32420.1 (Glycine max), 3'ss of exon 5
---tttgagaaaaaatcattgttttaggttaatacacttctccgcctt-ttttatctgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
|| | | | | || | || ||| |||| | | | | | || | |||| | || ||| | | ||| ||| | |||||||| ||||||||||||||||| || |||||||| |||||||| |||| ||||||||||||||||||||| |||||
tatcttatcatgagttgaacattacaagt--ataattttctacttataatcccaattattttaccttcaaattagg-atagaggctaagttc-tacatttgcagGTCATTGGCTGGTCAATGTGGTTTTCTGAGTATCTTTTTCTGGAGAGAAGTTGGGCCAAGGATGAAAGCACATTAAAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 5
-------tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatctgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
||||| | | | || || || || |||| | ||||| ||| | | || | || | | | || | | |||||||| || |||||||||||||| || || ||||| || ||||| |||| |||||||||||||||| |||| |||||
ggaagcttttgaacctgatttactggattcttttg-ta-gcttcattgataacattatcatttaaa-gtcaatgtgatctattagctaagttccaatg----tgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G12560.1 (Glycine max), 3'ss of exon 5
---tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatc--tgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
|| ||| | ||| || | || | || | | ||| |||| | | || | || | || || || | | |||||||| || |||||||||||||| || || ||||| || ||||| |||| |||||||||||||||| |||| |||||
aagcttttgaacc--tgatttacttggattcttttgtggcttcattgatgacatcattgtttaaagtcaatgttgatctattagctaagttcca---atgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
upper sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 5
----tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatctgttacatattcatagtactcataaacagaattt-tcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
| | | |||| || | | | | | | | |||| | || || |||| | || | |||| || | || | || ||||| ||||| |||||||||||||| || |||||| | |||||||||||||| ||||||||||||||||||| |||||
tagatgtcgtctgcatacatttttctttgcaattgctcattgaacactttgacacct-ctatatatatacagga----taaatgttatgtgtccaatttattcagGTGATAGGTTGGTCAATGTGGTTTTCTGAGTATTTATTTCTGGAAAGAAACTGGGCCAAGGATGAAAGCATAATAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatctgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
ataaacagaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatctgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - -gaaaaaa
- - - - - - - - -gttttag
- - - - - - - - - - - - - -aatacac
- - - - - - - - - - - - - - - - - ttctccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataaac