Sequence
atgc intronic sequence ATGC exonic sequencegtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G59610.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 19
--------gtggactagtcacttttcttgtgaattct--taaattcccatgccaatatcgcttttcattactcgatcacattactaa-atctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
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gtttacatttgaacctcacaattgtttcaacagtcatactattttttaaactcaatttaacatggtcatagttgcaattgttattattgtctttttcatgatcagGCAATCGTACTTTGCCAAGTGGAGAAAGCAAAGGAAGATATGCTAAATCAGCTCTACAGCAAAATAAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 19
gtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
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--------------gttcatattggtctgtcaa--ccagtttaaatggccttttatttgtgtcaaattc-ttattgtttgtctgtacttgttagGCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 7
gtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
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--------gttcatattgttctg--ttaatcagtttaaatggccttgta----tttgtgtcaaattttcattgcttg-tctgta--cttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 19
gtggactagtcacttt-tcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
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--------gtgagtttattttatcaactaccatagttcttctc---ttctgatttgatgtggtttgtgagatcatttcactttgg--ttgagcagGCAGTTGTTCTTTGCCAAGTAGAGAAAGCCAAAGAAGACATGCTGAACCAGCTATACAGTTCCGTCAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 19
gtggactagtcacttt-tcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
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--------gtgagtttattttatcaactaccatagttcttctct--tctgatttgacgcggtttg-tgagatgatttcactt-tgactg-agcagGCAGTTGTTCTTTGCCAAGTAGAGAAAGCCAAAGAAGACATGCTCAACCAGCTATACAGTTCCATCAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 19
gtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgctttt-cattactc---gatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
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----gtcggtttgttttcttaaatccattatgattcatgtattt-tgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcagGCAGTTGTCCTTTGCCAAGTAGAAAAATCCAAGGAAGATATGCTTAATCAGTTATACAGTTCTGTCAG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
gtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgact--tcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
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-----gtaagcacttgtccc-tgaattctcatttttgcatctttacat--ctggtcact-tacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAGMapped 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|164200292|gb|ES066203.1|ES066203EST: ACAGTCTAGCTGCCAATGTTCCAAAG GCTGTTGTTCTTTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAG
genomic: ACAGTCTAGCTGCCAATGTTCCAAAGgtggactagt ... acttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
tactaaa putative branch site (score: 1)
attactaaat 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
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gtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC