Sequence
atgc intronic sequence ATGC exonic sequencegttagaatctttcctaattctttaccttccaatgtagaatccatggagcaaagaactaaaaaaacgtggcatgtttttattttaactacagATTCTGAAATGCTGAAGGATGTTTCGAGATTAACAAGACAAGAGCTCGAAGTGGCGTGTGAAGACTTTAGCAACATCATTGGTTTATCAGCAGATAGTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63430.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G119759_T03 (Zea mays), 3'ss of exon 7
gttagaatctttcctaattctttaccttccaat-gtagaatccatggagcaaagaactaaaaaaacgtggc-atgtttttattttaactacagATTCTGAAATGCTGAAGGATGTTTCGAGATTAACAAGACAAGAGCTCGAAGTGGCGTGTGAAGACTTTAGCAACATCATTGGTTTA--TCAGCAGATAGTCA
|| || | | | | | || || | | ||||| || | | || | | | || | || || ||||||||||||| |||||||| | | | | ||||| | || ||||| |||||||| ||||| || ||||||||||||||||| | | || ||| ||
gtaagtgttaattacattgttcaacgggacagttggtgaatcgattaatgtgctttccaattattttggatgacgtatccatgttctctacagATTCTGATATGCTGAAAAGTCTACCAAAATTAAGTCGCCAGGAGCTTGAAGTGGCCTGTGAGGATTTTAGCAACATCATTGGCTCAACTCCAGAGACGGT--
upper sequence: AT1G63430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G349191_T01 (Zea mays), 3'ss of exon 3
gttagaatctttcctaattctttaccttccaat-gtagaatccatggagcaaagaactaaaaaaacgtggc-atgtttttattttaactacagATTCTGAAATGCTGAAGGATGTTTCGAGATTAACAAGACAAGAGCTCGAAGTGGCGTGTGAAGACTTTAGCAACATCATTGGTTTA--TCAGCAGATAGTCA
|| || | | | | | || || | | ||||| || | | || | | | || | || || ||||||||||||| |||||||| | | | | ||||| | || ||||| |||||||| ||||| || ||||||||||||||||| | | || ||| |||
gtaagtgttaattacattgttcaacgggacagttggtgaatcgattaatgtgctttccaattattttggatgacgtatccatgttctctacagATTCTGATATGCTGAAAAGTCTACCAAAATTAAGTCGCCAGGAGCTTGAAGTGGCCTGTGAGGATTTTAGCAACATCATTGGCTCAACTCCAGAGACAGT--
upper sequence: AT1G63430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA11G02690.1 (Glycine max), 3'ss of exon 8
---gttagaatct-ttcctaattctttaccttccaatgtagaatccatggagcaaagaactaaaaaaacgtggcatgtttttattttaactacagATTCTGAAATGCTGAAGGATGTTTCGAGATTAACAAGACAAGAGCTCGAAGTGGCGTGTGAAGACTTTAGCAACATCATTGGTTTATCAGCAGATAGTCA
|||| ||| || || ||| ||| ||| | | || | | | | ||| | || |||||| | | |||| |||| || |||| ||||| || | | ||||||||||| ||||| || ||||||||||| |||||||| ||||| | ||| ||||||||
gtatgtagattctgtttctttttccctactttctatt-tacatctagtatttctagagctgttttcaacataat-tggctttatta-atgtgcagACCCTGAGTTGTTGAAAGATGTGAGAAGGTATAGCAGACAAGAGCTTGAAGTTGCCTGTGAAGACTTCAGCAACATAATTGGGTCCTCACCAGATAGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatccatggagcaaagaactaaaaaaacgtggcatgtttttattttaactacagATTCTGAAATGCTGAAGGATGTTTCGAGATTAACAAGACAAGAGCTCGAAGTGGCGTGTGAAGACTTTAGCAACATCATTGGTTTATCAGCAGATAGTCA
ttttaac putative branch site (score: 2)
tttttatttt CT-rich tract
atgtttttattttaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaatctttcctaattctttaccttccaatgtagaatccatggagcaaagaactaaaaaaacgtggcatgtttttattttaactacagATTCTGAAATGCTGAAGGATGTTTCGAGATTAACAAGACAAGAGCTCGAAGTGGCGTGTGAAGACTTTAGCAACATCATTGGTTTATCAGCAGATAGTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT