Sequence
atgc intronic sequence ATGC exonic sequence...ctgcagtatgaggcttgattgagctgttccgttaaacacatttttccatattttatctaaatagatatttgattaatgattgtccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79000.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 6
ctgcagtatgaggcttgattgagctgttccgttaaacacatttttc-catattttatctaaatagatatttgattaatgattgt-ccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
| || || | ||| ||||| | | |||| | |||| | | ||| || || | | | || | || | | | ||||| || | |||||||| |||||||| |||||||||||||||||||||||||| ||||||||| | ||||| || ||||||||||||||||| ||||| |
-taaggtttgggtaagcattatattgttc-atgtggtatatttcccacataatatttctctatttatccacaagttgtcataacatcatcttcttgtgacagAGCAAGTCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGCCAATTGTGTGCTGTAGAGAAGCTTACCTTTGAACCACCGC
upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 8
--ctgcagtatgaggcttgat-tgagctgttccgttaaacacatttttccatattttatctaa-atagatatttgattaatgattgtccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
|| | | | || || || | || | | | |||| || | ||| ||||| || | || | | | | ||| ||| ||||| || | |||||||| |||||||| |||||||||||||||||||||||||| ||||| ||| | ||||| || ||||||||||||||||| ||||| |
tactagtttttaattgttcatgtggcatatttcctacatagtatttctcta-attatatctggtatccacatgttaccataacatcattttcttgt---cacagAGCAAGTCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTTGAGAAGCTTACCTTTGAACCACCGC
upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 6
ctgcagtatgaggcttgattgagctgttccgttaaa--cacatttttccatattt-tatctaaatagatatttgattaatgattgtccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
| |||| || | || | | | ||| | | || ||| || || | | || |||| | | ||| || | | | ||||| ||| | |||||||| |||||||| |||||||||||||||||||||||||| ||||| ||| | ||||| || || || || || ||||| ||| | |
-ttcagt-tgctgtatgtcctccttaattccttatagtcttatacttctttaattgtcttggtatcctaattttaccga-gatgcatctatttattgtgacagAGCAAATCAAAAGCAGAGAAGAATCAAGCAATGGAGCATTCAATGAGTGAGAACTCCTGTCAATTGTGTGCTGTAGAAAAACTAACTTTTGAACCATCCC
upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 5
---ctgcagtatgaggcttgattgagctgttccgttaaacacatttttccatattttatctaaatagatatttgattaatgattgtccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
||| | | || || |||| | | ||||| || ||| |||| | ||||| | | || | | | | || |||| || ||||| |||||||||||||| |||||||||| ||| ||||||||||| || || || || |||||||| ||||||||||| ||||| || ||||
tggctgttgagaatgatttttctgttttgtttttatttttat-tttttatgtactttgtctaggtttggtggtgattttttttcctcttcccttt--ttctagAGCAAGGCCAAGGCAGAAAAGAATCAAGCAATGGAGCGTTCGATGAGTGAGAACTCTTGTCAGCTGTGTGCAGTTGAGAAGCTTACTTTTGAACCTCCAC
upper sequence: AT1G79000.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S462_17V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------ctgcagtatgaggcttgattgagctgttccgttaaa----cacatttttccatattttatctaaatagatattt--gattaat-----gattgtccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATG---GAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
|| | | || || | || |||||| || |||| | |||| || | | ||| || | | | |||| || || | ||||| || ||||| || || ||||||||||| | ||| || ||| ||||||||| | |||||||||||||| ||||||||||| || || || || |
gtttagttctaattccacttctctcttgaagctccttttcttagcacacttcaaatggagcgttaagtttccagtgttttgaaggttttgactctcttgtgctttcagagcagtactaagtttgtgatttgggtacaaacagAGCAAGGCCAAGGCTGAGAAGAATCAGGCCCTCAGTGAGAATCAAATAAGTGAGAATGCATGCCAACTATGTGCTGTGGAGAAGCTAACATTCGAACCTC--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatattttatctaaatagatatttgattaatgattgtccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
gattaat putative branch site (score: 3)
ttttatctaaatagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgcagtatgaggcttgattgagctgttccgttaaacacatttttccatattttatctaaatagatatttgattaatgattgtccttcatgtgcttgcagAGTAAAGCCAAAGCAGAAAAGAATCAGGCAATGGAGCATTCAATGAGTGAGAATTCCTGCCAACTATGTGCAGTGGAGAAGCTTACCTTTGAGCCACCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC