Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttctcaatcttagtctcattctaaccaagcttagtgttttattctgtacacaactctaatatgacatgactgtcatatcttcgtagGTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34410.3 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34410.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os01g44040.1 (Oryza sativa), 3'ss of exon 12
gtatgt-ttctcaatct-tagtctcattctaaccaagcttagtgtttt----attctgtacacaactctaatatgacatgactgtcatatcttcgtagGTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAG
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gtaagtcttttcaaactataacctaaaactttttatatttaatttcctgtggattcactttgtcagactaaacttataaca-tactttttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAG
upper sequence: AT2G34410.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os01g44040.2 (Oryza sativa), 3'ss of exon 12
gtatgt-ttctcaatct-tagtctcattctaaccaagcttagtgtttt----attctgtacacaactctaatatgacatgactgtcatatcttcgtagGTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAG-------------------------------------------
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gtaagtcttttcaaactataacctaaaactttttatatttaatttcctgtggattcactttgtcagactaaacttataaca-tactttttaccaatagGTGGCTTGGCAAGATTACTCTGGAGACCTATATCTCTCAGATCCACATTTGGCTCAGGTATGATGCTAGCCTTTTGTGTTCAGTATGTGCTCCTATCTTT
upper sequence: AT2G34410.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 13
-------gtatgtttctcaatctt---agtctcattctaaccaagcttag-------tgttttattctg----tacacaactctaatatgacatgactgtcatatcttcgta---gGTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAG
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gtacgtgttctttaccttaattattgaaattccatgttaattggttttggatcattttgtttttatttggtgataagtatctttttttttctgaatttcccccacttttgtatcagGTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG
upper sequence: AT2G34410.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 13
-------------------------------gtatgtttctcaatcttag----tctcattctaaccaagcttagtgttttattctgtacacaactctaatatgacatgactgtcat-atcttcgt---agGTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAG
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gtatgtgttctttaccctaattattgaaattctatgttgattggttttggattattttgttttttatttggtgactgctatctttttttcttttttttttcttttctgaattttccccatttttgtatcagGTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG
upper sequence: AT2G34410.3 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------gtatgtttctcaatctta----gtctcattctaaccaagcttagtgttttattct-----------gtacacaactctaatatgacatgactgt--catatcttcgt------agGTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAG
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gtaagttctctttgatctatatgatttaagttgaatcatttgactcataacctcacaaaaatttatagtttagaaacattgttttttatatttagagataatagttaacaactctgatttctc-taactgtgccacacctttgtgcttctagTTGGCTTGGCAAGATCACTTTGGAGACTTATATTTCTCAATTCCACATCTGGTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtgttttattctgtacacaactctaatatgacatgactgtcatatcttcgtagGTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAG
ctctaat putative branch site (score: 3)
tatcttc putative PPT
ttttattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttctcaatcttagtctcattctaaccaagcttagtgttttattctgtacacaactctaatatgacatgactgtcatatcttcgtagGTGGCTCGGCAAGATTACTCTGGAAACCTATATTTCTCAGTTTCACATCTGGTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA