Sequence
atgc intronic sequence ATGC exonic sequence...ttgttataatcattacctataaattatacatgtagacttaagttgagaagtagtagttgcttgttttctttggcagcctctaacaaataattttttccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13160.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G44580.2 (Glycine max), 3'ss of exon 3
ttgttataatcattacctataaattatacatgtagactta-agttgagaagtagtagttgcttgttttctttggcagcctctaacaaataattttttc-----cagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
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-----aaaatgtttccttgtta-ttatatctgtcttcttatgattgactagtatctcatgctgataataactaatgtttaatcattatttatggactggagggcagATCTTCCCCCGGATAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCATGACAAAGCAAATCC
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G39370.2 (Glycine max), 3'ss of exon 2
---ttgttataatcattacctataaattatacatgtagacttaagttgagaagtagtagttgcttgttttctttggcagcctctaacaaataattttttccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
|| | | ||| ||||| || || ||| | || | | | | | ||| | | || | | |||||||||| ||||| ||||| | ||||||||||||| || ||||||||||||||||| || || ||||||||||||| || || || || ||||||||
taaactttgggtagagtggaaatacattattaccttaaacataa-tgcagttatgctgataataactaatgtttaatcattatttatgaac--tggagtgcagATCTTCCCCCGGACAAGGAACCATTAGATTGGAACACCAGGATGAAAATAGCTGCTGGGGCAGCAAAAGGATTGGAATACCTTCACGACAAAGCAAACCC
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G47570.1 (Glycine max), 3'ss of exon 3
ttgttataatcattacctataaattatacatgtagacttaagttgagaagtag---tagttgcttgttttctttggcagcctctaacaaataattttttccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
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atattttaaatagcatgttaatgtaaactgccttaacaaacaatatgcaattgccataatgacaattgatgtttaacattgtttattgatc---tctatgcagATCTTCCCCCTGATAAGGAACCACTAGATTGGAACACTAGAATGAAAATTGCTGTTGGTGCTGCAAAAGGATTAGAATACCTTCACGATAAGGCAAATCC
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G27350.1 (Glycine max), 3'ss of exon 3
---ttgttataatcattac-ctataaattatacatgtagacttaagttgagaagtagtagttgcttgttttctttggcagcctctaacaaataattttt--tccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
|| | | |||| || | | ||| | |||| | | || || | | || | | ||| | | | | |||| |||| || ||| | || | ||||||||||||| || ||||||||||||||||| || || |||| |||||||| || || | || ||||| ||
taaatgctgtgtattttacattacttccttcttaaacagaatgcagttatgt--tgataacaactaatatgttt----aatcattaattatggactccgagtgcagACCTTCTCCCAGATCAAAAGCCATTAGATTGGAACACAAGGATGAAAATAGCTGCTGGGGCAGCAAAAGTATTGGAATACCTTCACAACAAAGCAAATCC
upper sequence: AT5G13160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0146g00250.t01 (Vitis vinifera), 3'ss of exon 3
ttgttataatcattacctataaattatacatgtagacttaagttg-agaagtagtagttgcttgttttc-tttggcagcctctaac-aaat-aattttttccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
|| | |||| | | | ||| | | || | || ||| | || || | || | | ||| || || || |||| || ||| | ||||||||||||| |||||||| | | |||||||||| |||||||| ||||| |||||||| || || || ||||||| | ||||| || |||| |||
-tgct-taataa--atttgtaaccattgcctgatcatttcagtcacatgagctgttgccaattttagtaacttgtcaaccaatagttaaatgaactttgtgcagATCTTCCACCTGATAAGGAACCGCTGGATTGGAACACAAGAATGAAGATAGCAGCTGGTGCAGCCAAGGGTTTGGAATACTTGCATGACAAAGCAAGCCCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116483438|gb|EG526030.1|EG526030EST: CTTGGTCTACGAGTTTATGCCGTTAGGATCATTGGAAGATCACCTCCACG ATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAG
genomic: CTTGGTCTACGAGTTTATGCCGTTAGGATCATTGGAAGATCACCTCCACGgtaaatctct ... ttttttccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaagtagtagttgcttgttttctttggcagcctctaacaaataattttttccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
ctctaac putative branch site (score: 2)
ttttttcc putative PPT
tctaacaaataatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttataatcattacctataaattatacatgtagacttaagttgagaagtagtagttgcttgttttctttggcagcctctaacaaataattttttccagATCTTCCACCGGATAAGGAGGCCTTAGATTGGAACATGAGAATGAAAATAGCTGCTGGTGCGGCGAAAGGATTGGAATTTCTACATGATAAGGCAAACCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - cattacc
- - - - - - - - - - - - - - - - - - - - - - -agaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaataa