Sequence
atgc intronic sequence ATGC exonic sequencegtaataacttccacaacttttctattctccttctgtcattgcacaacattttcaaagtaaactgattaaaatctcgatacaaaaactcgttagGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G00630.2 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 18
--------gtaataacttccacaacttttctattctccttctgtcattgcacaacattttcaaagtaaactgattaaaatctcgatacaaaaactcgttagGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG
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gggcccattctttgtcttatgcatatccttttgttatatactgtattctatcaccgatttaataatactatc-tcctaatggaactacatctacttttaagGTTGTCCCTGAGACCTTGGAACCAAGTCTCCAGTTGGCTGCTGCTGTTCTTGCACAG
upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 21
gtaataacttccacaacttttctattctccttctgtca---ttgcac--aacattttcaa--agtaaactgattaaaatctcga---tacaaaaactcgttagGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG
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--aaagagttttgttgtttagtcttgctttttgtagcaaaattgaaacaaaaacttaccattagtgaaatgcttactctagagaactttctgccacatgc-agGTTGTCCCAGAGACCTTGGAACCAAGTCTTCAACTAGCAGCTGCTGTGCTTTCTCAG
upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 25
gtaataacttccacaacttttctattctccttctg-tcattgcacaacattttcaaagtaaactgatta------aaatctcgataca-aaaactcgtt---------agGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG-
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-----------aagagttttgttgttttagtcttgctttttgtagcaaaattgaaagaaaaacttaccattagtgaaatgcttatctagagaactttctgccacttgcaggTTGTCCCGGAGACCTTGGAACCAAGTCTTCAACTAGCAGCTGCTGTGCTTTCTCAGG
upper sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 16
---------------------------------------------------------------------------------------------gtaataacttccacaacttt--tctattctccttctgtcattgcacaacattttcaaagtaaac--tgattaaaatctcgataca------aaaactcgt-tagGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG
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gtatcattaattttactttccctttttctattctgtaattttttgacctcttgggcatttattgcattagttattgaaaatctacaactactaaaactaatacctattatcggagtatattttcttagggtttttgt-cttcccttctaaatcaccccttgacttttattttgcatcatctgttaaaaaacatacagGTTGTTCCAGAGACCTTGGAACCAAGTCTGCAGTTAGCTGCTGCTGTTCTTGCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcacaacattttcaaagtaaactgattaaaatctcgatacaaaaactcgttagGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG
aactgat putative branch site (score: 3)
taaactgattaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataacttccacaacttttctattctccttctgtcattgcacaacattttcaaagtaaactgattaaaatctcgatacaaaaactcgttagGTTGTTCCTGAGACGCTGGAACCAAGTCTTCAGTTAGCAGCTGCTGTTCTTGCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT