Sequence
atgc intronic sequence ATGC exonic sequence...ttagattgaaattatggactcagtttgctgttcatgtgatgagaaggatgcacgtttcatgtttaaattgattttgctaaagccctgtttatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50320.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 1
--ttagattgaaattatggactcagtt-tgctgttcatgtgatgagaaggatgcacgtttcatgtttaaattgattttgctaaagccctgtt---tatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
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caacagattgtgttgggcgatatagccatgaagttgtcgccattattttgac---tgcttcatccct---ttgggtttcagaactttctgatctgtctacttgtagGTACAATCCATATGTGCAGGCCAGAAGCAGGATAGATCAGCTCAAAAGGCTAGGCCATAGTGTAGACAAG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 1
ttagattgaaattatggac-tcagtttgctgttcatgtgatgagaaggatgcacgtttcatgtttaaattgat--tttgctaaagccctgtttatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
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tatgtttaaagctacagatgtttgtgcactgtgattat--ttaaactgatttgttgatacacttttggtcgataattttcttgatctacatttacattct-agGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGTTAGGGCATAGTGTGGATAAG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G359735_T03 (Zea mays), 3'ss of exon 1
----ttag--attgaaattatggactcagtttgctgttcatgtgatgagaaggatgcacgtttcatgtttaaattgattttgctaaagccctgtttatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
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atgtttagcgatacagatgattg-tgcacttcaattattttaaactgatttattcacacacttttcgt---agatgattttcctgatctaccatt-ata-ttttagGTATAATCCATATGTGCAAGCCAGGAGCAGGATAGATCAGCTCAAGAGGCTAGGGCATAGCGTGGATAAG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G36790.1 (Glycine max), 3'ss of exon 1
ttagattgaaattatggactcagtttgctgttcatgtgatgagaaggatgcac-gtttcatgtttaaattgattt----tgctaaagccctgtttatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
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ctagtctagttttat----tttgtgtacaac-cattctttgaagggtatacattgtgccttgtgctaatttttttatcatgatatacttatggaactggatttagGTATAATCCATATGTCCAAGCGAGGAGCAGGATAGATCAGCTTAAGCGTTTGGGTCATAGTGTAGACAAG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G18150.1 (Glycine max), 3'ss of exon 1
ttagattgaaattatggactcagtttgctgttcatgtgatgagaaggatgcacgtttcatgtttaaattgattttgctaaagccctgtttatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
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ttagtcttgttttatttcatgtacaaacattctttgaaggatttacattgtgccttgtgctatttttttatgaatgatatgattgtgtaactggatttagGTATAATCCATATGTCCAAGCGAGGTGCAGGATAGATCAGCTTAAGCGTTTGGGTCATAGTGTAGACAAG
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 3'ss of exon 1
---ttagattgaaattatggactcagtttgctgttcatgtgatgagaaggatgcacgtttcatgtttaaattgattttgctaaagccctgtttatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
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atcgttgcttatttttctgcaagaaaattcttgtaacttttcttttaacttt-tttgtgatatgctct--ctgtttctattttcttttctcttttggttgcagATATAACCCATATGTCCAGGCTAGAAGCAGGATCGATCAGCTGAAGCGGCTGGGTCATAGTGTAGACAAGMapped 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|301501204|gb|HO206744.1|HO206744EST: CAGTCTTACACTGGATATGAGCCTACCAGCATGCGAGCTATTCGAGCCAG GTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTT
genomic: CAGTCTTACACTGGATATGAGCCTACCAGCATGCGAGCTATTCGAGCCAGgtgaagagtg ... atggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTT
EST:
gi|163995707|gb|EL998894.1|EL998894EST: CAGTCTTACACTGGATATGAGCCTACCAGCATGCGAGCTATTCGAGCCAG GTACAATCCATATGTTCAGGCAAGAAGCAGGATAGA
genomic: CAGTCTTACACTGGATATGAGCCTACCAGCATGCGAGCTATTCGAGCCAGgtgaagagtg ... atggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatgcacgtttcatgtttaaattgattttgctaaagccctgtttatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
tgctaaa putative branch site (score: 2)
tttcatgtttaaattg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagattgaaattatggactcagtttgctgttcatgtgatgagaaggatgcacgtttcatgtttaaattgattttgctaaagccctgtttatggtcttagGTACAATCCATATGTTCAGGCAAGAAGCAGGATAGATCAGCTGAAGCGGTTGGGTCACAGTGTAGATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - -ctgttca
- - - - - - - - - - - - - - - - - - - - -agaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattttg