Sequence
atgc intronic sequence ATGC exonic sequence...tagatcatgtagatacaatgctgaatgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G22290.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
-------tagatcatgtagatacaatgctgaatgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
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aattatcttcttcgtaaatttgttttgcacaatgtttccatctccct-tcccccttttcctgctagggtcttgaca--aatttcttga----tcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
-tagatcatgtagatacaatgctgaatgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctc-ataaatctttgtttcat-----tcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
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atcttcttcgtaaatttgtt-ttgcatttgaatctttacgatctcc------cttcccccttttcctgctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 1
tagatcatgtagatacaatgctgaatgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtt---tcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
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-ttgttttcttggtatatttttttattccatcaacgattcacaatttttatgcttcctg--ctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
-tagatcatgtagatacaatgctgaa-tgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
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gtttccttggtatatatttttttgttctgtcaaggatccacaatttt--tattcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
upper sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
tagatcatgtagatacaatgctgaatgtaaatt-tcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
| | | | | | || | || || | ||| | ||| ||| | | ||| | |||||| | ||| |||| | | | |||||||| ||||| ||||| || || || ||||| ||||||||||| |||||||| ||||| ||||||| ||
-aaaaagaaaaaaaaaattggtttatctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctttttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
tctttgtttcattc CT-rich tract
acaaaatttatacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagatcatgtagatacaatgctgaatgtaaatttcttttagttgtagtaatcttcacaaaatttatacattagtctcataaatctttgtttcattcacagGCTACTATTGGAATTGACTTCTTATCGAAAACAATGTACCTTGAAGATCGAACTGTTCGTCTGCAGCTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - -gatacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tcacaaa