Sequence
atgc intronic sequence ATGC exonic sequence...ggaattatacagattgatgtgggtcaaatttgacatgattcatagagtagaaattgtgttaggcttgttcttatacgggagtgatttgcttcgtttgcagCATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACACCAGAGGTTGTTCTCAAGGCATCTGGGCATGTAGATAAGTTCACTGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G29880.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 1
ggaattatacagattgatgtgggtcaaatttgaca--tgattcatagagtagaaattgtgttaggctt---gttctta--tacgggagtgatttgcttcgtttgcagCATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACACCAGAGGTTGTTCTCAAGGCATCTGGGCATGTAGATAAGTTCACTGATC
|| | | |||| | || || |||||| | | || | | | || |||| || | | ||| || | | ||| ||| ||| ||||| ||| || | |||||||||||| | || ||||| || || |||||||| || |||||||| | |||||||| |||||||| || ||||| ||||| |
--tatgtttgaaattgct-tgtgt---atttgataactttttattttgattttacttatgttgggtactaagattttagtcaccaaattcattcttttctttt-cagCACTTCGTTTTGGAGGAGAACATGTTGGAGGTTGACTGCCCCTGTGTGACGCCTGAGGTTGTGTTGAAGGCATCGGGGCATGTCGAGAAGTTTACTGACC
upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 1
ggaattatacagattgatgtgggtcaaatttgacatgattcataga-gtagaaattgtgttaggcttgttctta-tacgggagtgatttgcttcgtt-----tgcagCATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACACCAGAGGTTGTTCTCAAGGCATCTGGGCATGTAGATAAGTTCACTGATC
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-------tgcacatttatacgaatgctggcatatgtagtgcatgaatatataaaattcaatacaattcctttgaatgtattgttgatccactctattcttttttcagCATTTTGTTCTTGAGGAGAACATGTTGGAAGTTGACTGCCCTTGTGTAACGCCTGAAGTTGTTCTGAAGGCTTCAGGGCATGTTGATAAATTTACCGACCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116404822|gb|EG447414.1|EG447414EST: GTCCTCCTGGCTGTGCTATTAAATCCAATGTTCTCAGCTTTTGGCGTCAA CATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACA
genomic: GTCCTCCTGGCTGTGCTATTAAATCCAATGTTCTCAGCTTTTGGCGTCAAgtaaggaaca ... tcgtttgcagCATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACA
EST:
gi|125221091|gb|EL235176.1|EL235176EST: CTTTTGGCGTCAA CATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACA
genomic: CTTTTGGCGTCAAgtaaggaaca ... tcgtttgcagCATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtagaaattgtgttaggcttgttcttatacgggagtgatttgcttcgtttgcagCATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACACCAGAGGTTGTTCTCAAGGCATCTGGGCATGTAGATAAGTTCACTGATC
tttgcttc CT-rich tract
ttcttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaattatacagattgatgtgggtcaaatttgacatgattcatagagtagaaattgtgttaggcttgttcttatacgggagtgatttgcttcgtttgcagCATTTCATTCTTGAGGAGAACATGCTAGAAGTTGATTGTCCATGTGTGACACCAGAGGTTGTTCTCAAGGCATCTGGGCATGTAGATAAGTTCACTGATC
- - - atacaga
- - - - - - - - - - - - - - - - - - - - - - - gtagaaa