Sequence
atgc intronic sequence ATGC exonic sequence...tttttaaattcgagatttggttatccatttgcgaagacaatgtctttcacttctatacgaaattcttaacgattggtttaaaatgctgaaaaaattgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAAGGTCTGCCTGTTGCTCTTGTCGAGTACGAAGGAGAACAACACGGTTTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G36210.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA18G11480.1 (Glycine max), 3'ss of exon 16
-tttttaaattcgagatt-tggttatccatttgcgaa--gacaatgtctttc-acttctatacgaaattcttaacgattggttt----aaaatgctgaaaaaattgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAAGGTCTGCCTGTTGCTCTTGTCGAGTACGAAGGAGAACAACACGGTTTTC
|| ||| | ||| | || ||| || | | | | | | || | | |||||| ||| | || || || || || | |||||||||||| | || |||||| | || ||||| || | || | || |||||||| |||| ||||||||||| ||||| |||||||||||||||||||| |
gttagtaacaatgctattattattttcccttaccatattgtctacttattcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 16
------------------------------------tttttaaattcgagatttggttatccatttgcgaagacaatgtctttcacttctatacgaaattcttaacgattggttt----aaaatgctgaaaaaattgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAAGGTCTGCCTGTTGCTCTTGTCGAGTACGAAGGAGAACAACACGGTTTTC
|| ||| | || | | | | | | || || || || || | | ||| ||| | || ||| | | | |||||||||| | ||||| ||| | || ||||| || | || | ||| |||| ||| |||| ||||||||||| |||||||||||||||||||| ||||| |
gttagcaacaattgcaactattttcctttcacatatttattacttaaaggactctggagtggaaattgtcaacttattcctaaatctactctatattactgataaaaattaatccgataaatatgtcttacacaatgcagGTTGTGCCCCCAGAACAAGCTCGGAAAATTTACCAGGCTCTGAAGGAAAAGGGTGTGCCAGTTGCTCTTGTTGAGTACGAAGGAGAACAACATGGTTTCC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 3'ss of exon 16
tttttaaattcgagatttggttatccatttgcgaag---acaatgtctttcacttctatacgaaattcttaacgattggtttaaaatgctgaaaaaa-ttgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAAGGTCTGCCTGTTGCTCTTGTCGAGTACGAAGGAGAACAACACGGTTTTC
| | |||| | | | | | | ||||| || | ||| | | || | | | |||||| ||| |||||||||||| |||||| |||| | ||||||||||| | ||||| ||| |||| ||| |||||||||||||||| ||||| |||||||||||||| || ||||
----ccagtaatggattgcataaagaagtagtgggttccacaatatcgcccttttcagcattgattttgttcctgaatttctaaaatctcataaattcttgcagGTTGTACCTCCAGTTCAAGCTCGTAAAATCTACCAGGCATTGAAGGAAAAGGGTTTGCCTGTTGCTCTTGTGGAGTATGAAGGAGAACAACATGGATTTC
upper sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 3'ss of exon 16
tttttaaattcgagatttggttatccatttgcgaagacaatgtctttcacttctatacgaaattcttaacgattggtttaaaatgctgaaaaaatt--gcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAAGGTCTGCCTGTTGCTCTTGTCGAGTACGAAGGAGAACAACACGGTTTTC
| | | | || ||| || | || | | | ||| | | | | | || ||| ||| |||| || |||||| ||| | ||||| ||| | ||||||||||| ||| | |||||||||||| |||||||||||||||| |||| |||||||||||||| |||||||
catctgcaatggactattgacta--aagcagcaggttccactacattcccatttttcagcaacatttagttccaaatttgaaatttctcgtcttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAAGGTTTGCCTGTTGCTCTTGTGCAGTATGAAGGAGAACAACATGGTTTTCMapped 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|86087244|gb|DR383003.1|DR383003EST: TCGATAAGTTCTCTTGTCCCATCATCCTTTTCCAAGGACTAGAAGACAAG GTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAA
genomic: TCGATAAGTTCTCTTGTCCCATCATCCTTTTCCAAGGACTAGAAGACAAGgttcttatat ... aaaattgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAA
EST:
gi|86087701|gb|DR383460.1|DR383460EST: TCGATAAGTTCTCTTGTCCCATCATCCTTTTCCAAGGACTAGAAGACAAG GTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAA
genomic: TCGATAAGTTCTCTTGTCCCATCATCCTTTTCCAAGGACTAGAAGACAAGgttcttatat ... aaaattgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcacttctatacgaaattcttaacgattggtttaaaatgctgaaaaaattgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAAGGTCTGCCTGTTGCTCTTGTCGAGTACGAAGGAGAACAACACGGTTTTC
tcttaac putative branch site (score: 2)
aaattcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttaaattcgagatttggttatccatttgcgaagacaatgtctttcacttctatacgaaattcttaacgattggtttaaaatgctgaaaaaattgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAAGGTCTGCCTGTTGCTCTTGTCGAGTACGAAGGAGAACAACACGGTTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - -gatttgg
- - - - - - - - - - - - - - - - gaagaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgaaatt