Sequence
atgc intronic sequence ATGC exonic sequence...cataattttcttggttcaatacaggaagtgacctggttatttgctgatgcttatttttaagttcttattacattattgaaattgtccaactggtaggaagGTTCAAGGCTACTGATGCAGGAAGATTGCGAGCTGAATACAACCGGCTGGTTGAGGGTTTAGCACTGAGAGGGGACTTATCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03190.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 2
cataattttcttggttcaatacaggaa--gtgacctggttatttgctgatgcttatttttaagttcttatt-acattattgaaattgtcc-------aactggtaggaagGTTCAAGGCTACTGATGCAGGAAGATTGCGAGCTGAATACAACCGGCTGGTTGAGGGTTTAGCACTGAGAGGGGACTTATCTG
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----------cctgtgcaatagtgccattattgctttattttccatttgtacccatagctgaaatttgattcagattctcttaactatcggaatttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTTGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 2
cataattttcttggttcaatacaggaagtgacctggttatttgctgatgcttatttttaagttcttatt-acattattgaaattgtcc-------aactggtaggaagGTTCAAGGCTACTGATGCAGGAAGATTGCGAGCTGAATACAACCGGCTGGTTGAGGGTTTAGCACTGAGAGGGGACTTATCTG
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-------cctgtgcaatagtgccataattg-ctttattttccatttgtatccatagctgaaatttgattcagattctcttaactatcggaatttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTCGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 2
--cataattttcttggttcaatacaggaagtgacctggttatttgctgatgcttatttttaagttcttattacattattgaaattgtccaac-tggtaggaagGTTCAAGGCTACTGATGCAGGAAGATTGCGAGCTGAATACAACCGGCTGGTTGAGGGTTTAGCACTGAGAGGGGACTTATCTG
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ttcactaatttgcagatt-actactttatgttgtttc-ttttcttctgtcattagaaatgaagtttgttacagttcatt-aaattgtttgacatggtaggaagGTTCAAGGCCACTGATGCGGGTAGATTGAGAGCAGAATACAACAGGCTTGTTGAGGGTTTGGCCCAGAGGGGAAACTTACCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgcttatttttaagttcttattacattattgaaattgtccaactggtaggaagGTTCAAGGCTACTGATGCAGGAAGATTGCGAGCTGAATACAACCGGCTGGTTGAGGGTTTAGCACTGAGAGGGGACTTATCTG
tgctgat putative branch site (score: 3)
ttatttttaagttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataattttcttggttcaatacaggaagtgacctggttatttgctgatgcttatttttaagttcttattacattattgaaattgtccaactggtaggaagGTTCAAGGCTACTGATGCAGGAAGATTGCGAGCTGAATACAACCGGCTGGTTGAGGGTTTAGCACTGAGAGGGGACTTATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG