Sequence
atgc intronic sequence ATGC exonic sequence...tctaaattaatttacagatatcttacatcatgatttaccatacttagtttttttcgtcccttgcttaaagtggataattctttttgtgtgaaatctgtagAGGCATGGTGGCTGGACGTGGGGTGGAGGTAATCTCAGTAGTATGTCTGCTTCAGTATCCGTGCTTGGAGATAGTGGTTGGTTGAGTCACATTCAGAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04540.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G34510.1 (Glycine max), 3'ss of exon 6
tctaaattaatttacagatatcttacatcatgatttaccatacttagtttttttcgtcccttgcttaaagtggata---attctttttgtgtgaaatctgt--agAGGCATGGTGGCTGGACGTGGGGTGGAGGTAATCTCAGTAGTATGTCTGCTTCAGTATCCGTGCTTGGAGATAGTGGTTGGTTGAGTCACATTCAGAGCA
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--atgattagcttgattaacttgtggggcatcaattcataaagtctgtcttttaaat---ttatgtgaattgtattcccactctgtttctatgaattctatttagAGACAAGGTGGGTCAACGTGGGGTGGTGGCAATCTAAGTAGTATGTCTGCTTCGGTATCAACCCTTGGGGACAGTGGATGGTTACTACATGTTCAGAATG
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G33040.1 (Glycine max), 3'ss of exon 6
tctaaattaatttacagatatcttacatcatgatttaccatacttagtttttttcgtcccttgcttaaagtggata---attctttttgtgtgaaatctgt--agAGGCATGGTGGCTGGACGTGGGGTGGAGGTAATCTCAGTAGTATGTCTGCTTCAGTATCCGTGCTTGGAGATAGTGGTTGGTTGAGTCACATTCAGAGCA
| | | | | | | ||| || | | | || | || | || | || || || | ||| ||| | |||| | | | |||| || ||||| | || |||||||| || ||||| ||||||||||||||||| ||||| ||||| || ||||| ||||| || ||||||
--tggttggctagattaactttgtggggcatcgattcataaagtctgtctcttaaat---ttatgtgaattgcattcccactctgtttctatgaattttatttagAGACAAGGTGGGTCAACATGGGGTGGTGGCAATCTAAGTAGTATGTCTGCTTCGGTATCAACCCTTGGGGACAGTGGATGGTTACTACATGTTCAGAATG
upper sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv13s0074g00300.t01 (Vitis vinifera), 3'ss of exon 12
tctaaattaatttacagatatcttacatcatgatttaccatacttagtttttttcgtcccttgcttaaagtggataattctttttgtgtgaa------atctgtagAGGCATGGTGGCTGGACGTGGGGTGGAGGTAATCTCAGTAGTATGTCTGCTTCAGTATCCGTGCTTGGAGATAGTGGTTGGTTGAGTCACATTCAGAGCA
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---aaagtga--tgaaaattttttgaggcctt-tttgccaaactttagcatgaatatcaagtatgtacggggatcaaacatgtgtttatacattggttattgacagAGACATGGTGGATGGAGTTGGGGCGGAGGCAACCTCAGCAGTATGTCTGCTTCGGTATCAACGCTTGGAGACAGTGGTTGGTTAATACATGTTCAAAGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttttttcgtcccttgcttaaagtggataattctttttgtgtgaaatctgtagAGGCATGGTGGCTGGACGTGGGGTGGAGGTAATCTCAGTAGTATGTCTGCTTCAGTATCCGTGCTTGGAGATAGTGGTTGGTTGAGTCACATTCAGAGCA
ataattctttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctaaattaatttacagatatcttacatcatgatttaccatacttagtttttttcgtcccttgcttaaagtggataattctttttgtgtgaaatctgtagAGGCATGGTGGCTGGACGTGGGGTGGAGGTAATCTCAGTAGTATGTCTGCTTCAGTATCCGTGCTTGGAGATAGTGGTTGGTTGAGTCACATTCAGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - -cttacat
- - - - - - - - - - - - - - - - - - -ccatact