Sequence
atgc intronic sequence ATGC exonic sequencegttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatgattaatgtggcattgccactactaagtaccaaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G77440.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G42830.1 (Glycine max), 3'ss of exon 1
gttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatgattaatgtggcattgccactactaagtaccaaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
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------------gtatccaatcaaattctgtt-tcggattatgcacttttatagatagatgacatgcataattctattttatcactctaaaaactgaatacattcttttgcatttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAACCATTCATTTGCACAATGGATGCCATTGGAGCAAA
upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G11930.1 (Glycine max), 3'ss of exon 1
--gttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatgattaatgtggcattgccactactaagtaccaaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
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gtatcaatcaattgtgtt----tcggattaggctaattatgtttgattt--tatagatgatatgcacaattctattttatgta----tgtaaaaacaaattacactgttttgcctttcagGTTTGGTCCATACTTTTGCCAGCCTGTAATTGCTGGACTAGGAGATGATGACAAGCCATTCATTTGCACAATGGATGCCATTGGAGCAAA
upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G24270.3 (Glycine max), 3'ss of exon 2
gttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatga----ttaatgtggcattgccactactaagtaccaaattcttta--tttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
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-----------------------cagtaaactgtgagatttaaaattt-tcttgttattttaaattgttaataaactcttttttggaacagtgaaaacaaagtttgcgttcttttgcttttcagGTTTGGTCCATATTTTTGCCAGCCTGTAATTGCTGGATTAGGGGATGAAGACAAACCATTCATTTGCACAATGGATTGTATTGGCGCAAA
upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G10130.1 (Glycine max), 3'ss of exon 2
gttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatga----ttaatgtggcattgccactactaagtac-caaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
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----------------------acagtaaagcataagatttaaaattt-tcttgttatactaatttgttaataaactctaatttggaacagtgaaaacaaagtttgcattttttgcttttcagGTTTGGTCCATACTTTTGTCAGCCTGTAATTGCTGGATTAGGGGATGAAGACAAACCATTCATCTGCACAATGGATTGTCTTGGGGCAAA
upper sequence: AT1G77440.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 3
gttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatgattaatgtggcattgccactactaagtaccaaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
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----------catcattgtcaccctccct-ttataagc----actgttttctttggtgtctgtatgatttcaatgaagatgatat--gcatttctgaatataatgtttttt-ttttagGTTTGGTCCATACTTCTGCCAGCCTGTGATTGCTGGATTGGGAGATGAAGACAAGCCATTCATTTGCACAATGGATTCAATTGGAGCCAAMapped 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|86076869|gb|DR372626.1|DR372626EST: AAGCCTGAAACTTTCGCTAGTCTTGTATCGGCTATTCTTTATGAGAAAAG ATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAA
genomic: AAGCCTGAAACTTTCGCTAGTCTTGTATCGGCTATTCTTTATGAGAAAAGgttggtgaaa ... tttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAA
EST:
gi|124708666|gb|EH800068.1|EH800068EST: AAGCCTGAAACTTTCGCTAGTCTTGTATCGGCTATTCTTTATGAGAAAAG ATTTGGCCCATCCTTGTGCCAA
genomic: AAGCCTGAAACTTTCGCTAGTCTTGTATCGGCTATTCTTTATGAGAAAAGgttggtgaaa ... tttatttcagATTTGGCCCATTCTTGTGCCAA
EST:
gi|116388094|gb|EG430686.1|EG430686EST: AAGCCTGAAACTTTCGCTAGTCTTGTATCGGCTATTCTTTATGAGAAAAG ATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAA
genomic: AAGCCTGAAACTTTCGCTAGTCTTGTATCGGCTATTCTTTATGAGAAAAGgttggtgaaa ... tttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttatgattaatgtggcattgccactactaagtaccaaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
gattaat putative branch site (score: 3)
ttctttatttc putative PPT
aaattctttatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgaaatgtcttcttctctcaatttgttattagtttctagtttcctcttaacaatctgatttcttatgattaatgtggcattgccactactaagtaccaaattctttatttcagATTTGGCCCATTCTTGTGCCAACCTGTGATTGCTGGATTGGGAGATGATAACAAACCCTTCATTTGCACTATGGATTCTATTGGAGCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG