Sequence
atgc intronic sequence ATGC exonic sequence...ctgtctctgttcatccactaacatttcttcccatcatccatgcacatttggcttttatgttggcttagttggtctaacgaagcttccttttgatttttagATGTCGTGAGAAGCAGAGGAAAGAAGCTGCTCGTCTTCAAACAGTGAACAGAAAACTCAATGCCATGAACAAACTCTTGATGGAAGAGAATGATCGTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34710.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 1
----------------------------------ctgtctctgttcatccactaacatttcttcc-catcatccatgcac---atttggcttttatgttggcttagttggtctaacgaagcttcc--ttttgatttt---------------tagATGTCGTGAGAAGCAGAGGAAAGAAGCTGCTCGTCTTCAAACAGTGAACAGAAAACTCAATGCCATGAACAAACTCTTGATGGAAGAGAATGATCGTTTG
||| | ||| || || | | ||| || | | || || || | | ||| || ||| || | | || || || |||||| || ||| |||||||||||||||||||| |||||| |||| || || |||||||||||||| || | ||| |||||||| || || ||||| || ||||| ||||||
gtcagaccctatttttcaaataacccaaatgccaaaatcttttttcttcttcttatacttcctctataaaagccttgaacttcacctatttttcatcttgtctcaataaaagaaagcaactttttgtttttgacattggggaatttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGGCTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTTTTAATGGAGGAAAATGACCGTTTG
upper sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------------------------ctgtctctgttcatccactaacatttct-tcccatcatccatgcacatttggcttttatgttgg------cttagttggtctaacgaagcttcc-----ttttgatttttagATGTCGTGAGAAGCAGAGGAAAGAAGCTGCTCGTCTTCAAACAGTGAACAGAAAACTCAATGCCATGAACAAACTCTTGATGGAAGAGAATGATCGTTTG
|| || || | | | || | | | || ||| | | ||| ||| || ||| ||| | | || | ||||| | | ||| |||||||||||||||||||| |||||| |||| | || |||||||||||||| || | ||| |||||||| || || ||||| |||||||| ||||||
gtgtctttcttttcaaaatttcaaataacccaaatgccaaaatctcccatttcttattcttcctcaaaaaaagccttcaacttcacctattttttttatcttgtctcaatgaaagaacgcaactttttttagttcctattttgtgtttctttttattgttcttagaaggcattggtgaattttggtgtgtagGTGTCGTGAGAAGCAGAGGAAGGAAGCTTCTCGCTTGCAGACAGTGAACAGAAAGCTGACTGCAATGAACAAGCTGTTAATGGAGGAGAATGACCGTTTG
upper sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 1
--ctgtctctgttcatccactaacatttcttcccatcatccatgcacatttggcttttatgttggcttagttggtctaacgaagcttcc--ttttgatttttagATGTCGTGAGAAGCAGAGGAAAGAAGCTGCTCGTCTTCAAACAGTGAACAGAAAACTCAATGCCATGAACAAACTCTTGATGGAAGAGAATGATCGTTTG
|| || | | ||| | | | | ||| | || |||| || | ||| | || || |||| | | |||||||||||| |||||| |||| ||||| ||||||| || |||||||| ||||| || ||| |||||||| | |||||||||||||| || || ||
acttgagagagtgaaatgaataatgaatgactataata-caatgttatggtaaattctatgggaa---agattacctactctacctgccaattttcttctgtagATGTCGTGAAAAGCAGCGGAAGGAAGCCTCTCGTCTGCAGACAGTGAATAGAAAGCTGTCTGCAATGAACAAGTTGTTGATGGAAGAGAACGACCGACTG
upper sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 1
-ctgtctctgttcatccactaacatttcttcccatcatccatgcacatttggcttttatgttggcttagttggtctaacgaagcttccttttgatttttagATGTCGTGAGAAGCAGAGGAAAGAAGCTGCTCGTCTTCAAACAGTGAACAGAAAACTCAATGCCATGAACAAACTCTTGATGGAAGAGAATGATCGTTTG
| | | | |||| ||| | || | || || | | | || || || |||| | | |||||||||||| |||||| |||| ||||| ||||||| || |||||||| ||||| || | | |||||||| | || ||||||||||| || || ||
gaaatgaataatgaatgactatcatacaatgttatggtaaat-tgtatgggaaagatgacctactctacctgccttatactctgccaattttcttctgtagATGTCGTGAAAAGCAGCGGAAGGAAGCCTCTCGTCTGCAGACAGTGAATAGAAAGCTGTCTTCAATGAACAAGTTGTTAATGGAAGAGAACGACCGACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttggcttttatgttggcttagttggtctaacgaagcttccttttgatttttagATGTCGTGAGAAGCAGAGGAAAGAAGCTGCTCGTCTTCAAACAGTGAACAGAAAACTCAATGCCATGAACAAACTCTTGATGGAAGAGAATGATCGTTTG
cttccttttgattttt CT-rich tract
ttttgattttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctgtctctgttcatccactaacatttcttcccatcatccatgcacatttggcttttatgttggcttagttggtctaacgaagcttccttttgatttttagATGTCGTGAGAAGCAGAGGAAAGAAGCTGCTCGTCTTCAAACAGTGAACAGAAAACTCAATGCCATGAACAAACTCTTGATGGAAGAGAATGATCGTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - ctgttca
- - - - - - - -cactaac
- - - - - - - - - - - - - - -cccatca
- - - - - - - - - - - - - - - - - - -ccatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaag