Sequence
atgc intronic sequence ATGC exonic sequence...tcatattcaactgattgtctaataaagacagttgctttagctctgttattcacgaggattgtctcaagaagtttctaaagttggtagcatgtgtttgtagAATCTGAGATGGGCGAGCCACTAGGACTGCTCCAGGTGACTGTTATTCAAGGAAAGAAACTGGTGATCCGAGATTTCAAGTCAAGTGATCCTTATGTGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G47710.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G47710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G01720.2 (Glycine max), 3'ss of exon 1
--tcatattcaactgattgtcta-ataaa-gacagttgctttagctctgttattcacgaggattgtctcaagaagtttctaaagttggtagcatgtgtttgtagAATCTGAGATGGGCGAGCCACTAGGACTGCTCCAGGTGACTGTTATTCAAGGAAAGAAACTGGTGATCCGAGATTTCAAGTCAAGTGATCCTTATGTGAT
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tttttttttttgtttgtttcctacatgaacggtggatatttcaactgctttttttgt-agtgtggtatgatccatgcttgattaatagtttaacttgttagAAGGAG-TATCATGGGTGAACAATTAGGGCTACTAAAAGTCATGGTTGTGCAAGGGAAAAGGTTGGTGATCCGGGATTTCAAGACCAGTGATCCTTATGTA--
upper sequence: AT5G47710.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA15G12690.1 (Glycine max), 3'ss of exon 1
tcatattcaactgattgt--ctaataaagacagt---tgctttagctctgttattcacgaggattgtctcaagaagtttctaaagttggtagcatgtgtttgtagAATCTGAGATGGGCGAGCCACTAGGACTGCTCCAGGTGACTGTTATTCAAGGAAAGAAACTGGTGATCCGAGATTTCAAGTCAAGTGATCCTTATGTGAT
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ttgttttgttttgtttgtttccgacatgaacggtgaatatttcaactgtttttttttgtagtgtggtat--accatgtttgactattagtttaacttgttagAAGGAG-TATAATGGGTGAACAATTGGGGCTGCTAAAAGTCATTGTTGTGCAAGGGAAAAGGTTGGTGATCCGGGATTTCAAGACCAGTGATCCTTATGTT--Mapped 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|19875004|gb|AU235835.1|AU235835EST: AATTCATCACAACCACAAGAAGACGATTTTTTATTCTTGTTTCCAAACTG AATCTGAGATGGGCGAGCCACTAGGACTGCTCCAGGTGACTGTTATTCAAG
genomic: AATTCATCACAACCACAAGAAGACGATTTTTTATTCTTGTTTCCAAACTGgtaaagttgt ... gtgtttgtagAATCTGAGATGGGCGAGCCACTAGGACTGCTCCAGGTGACTGTTATTCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattcacgaggattgtctcaagaagtttctaaagttggtagcatgtgtttgtagAATCTGAGATGGGCGAGCCACTAGGACTGCTCCAGGTGACTGTTATTCAAGGAAAGAAACTGGTGATCCGAGATTTCAAGTCAAGTGATCCTTATGTGAT
ttctaaa putative branch site (score: 2)
tttctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatattcaactgattgtctaataaagacagttgctttagctctgttattcacgaggattgtctcaagaagtttctaaagttggtagcatgtgtttgtagAATCTGAGATGGGCGAGCCACTAGGACTGCTCCAGGTGACTGTTATTCAAGGAAAGAAACTGGTGATCCGAGATTTCAAGTCAAGTGATCCTTATGTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA