Sequence
atgc intronic sequence ATGC exonic sequenceAGCGCTTGCTCTAGAAGCTGAGGTTATGAAAAACCCTGAGAATGCTGAAGGTTGGAGATTACTTGGGGTCACACACGCAGAGAACGATGATGATCAACAGgttagttagattaatttgcatgaatattaatctcctataccttatcaaaatgatgaaacttagtcaattttcaaaacaattgtcgttgtggatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56290.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os08g39080.2 (Oryza sativa), 5'ss of exon 8
AGCGCTTGCTCTAGAAGCTGAGGTTATGAAAAACCCTGAGAATGCTGAAGGTTGGAGATTACTTGGGGTCACACACGCAGAGAACGATGATGATCAACAGgttagttagattaatttgcatgaatattaatctcc-tataccttatcaaaatgatgaaacttagtcaattttcaaaacaa--ttgtcgttgtggatgcag--
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TGTTCTTGCTTTAGAGGCTGAAGTTTTGAAGAATCCTGATAATGCTGAAGGTTGGAGACTACTTGGAGTAACACATGCTGAAAATGATGATGACCAACAGgtgattgtgtctctcccac-tgaggatatatgtagatgtaaattaccatg-tgctgattattttcaacttttcattattagtttttcagcacaggtgcactg
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G115855_T01 (Zea mays), 5'ss of exon 9
AGCGCTTGCTCTAGAAGCTGAGGTTATGAAAAACCCTGAGAATGCTGAAGGTTGGAGATTACTTGGGGTCACACACGCAGAGAACGATGATGATCAACAGgttagttagattaatttgcatgaatattaatctcctataccttatcaaaatgatga-aacttagtcaattttcaaaacaattgtcgttgtggatgcag------
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TGTTCTTGCTTTAGAGGCTGAAGTTTTGAAGAATCCTGATAATGCTGAAGGTTGGAGGTTGTTAGGCATAACACATGCAGAAAATGATGATGACCAACAGgtgacatatctcc-tttaaatgttta--aatctttcatat-taattaggatcatattaaaatacacgataggcaaccctgcacttgaagcatatatgcactgtc
upper sequence: AT5G56290.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv19s0015g01940.t01 (Vitis vinifera), 5'ss of exon 9
AGCGCTTGCTCTAGAAGCTGAGGTTATGAAAAACCCTGAGAATGCTGAAGGTTGGAGATTACTTGGGGTCACACACGCAGAGAACGATGATGATCAACAGgttagttagattaatttgcatgaatattaatctcctataccttatcaaaatgatgaaacttagtcaattttcaaaacaattgtcgttgtggatgcag---------
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AGTACTTGCATTAGAGGCTGAAGTTCTAAAAAACCCAGACAATGCTGAAGGTTGGAGGTTACTTGGAATAGCACATGCAGAGAATGATGATGATCAACAGgttgtgcaaatttgctgattttaa----ggcattctttaccttctttt--ccatgacatattttctgtgttgttaatcatggttgtgaagaaaaaagtccagtctaMapped 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|125213488|gb|EL228320.1|EL228320EST: ACTTGGGGTCACACACGCAGAGAACGATGATGATCAACAG GCAATAGCTGCAATGATGCGTGCACAGGAGGCTGATCCCACAAA
genomic: ACTTGGGGTCACACACGCAGAGAACGATGATGATCAACAGgttagttaga ... gtggatgcagGCAATAGCTGCAATGATGCGTGCACAGGAGGCTGATCCCACAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGCGCTTGCTCTAGAAGCTGAGGTTATGAAAAACCCTGAGAATGCTGAAGGTTGGAGATTACTTGGGGTCACACACGCAGAGAACGATGATGATCAACAGgttagttagattaatttgcatgaatattaatctcctataccttatcaaaatgatgaaacttagtcaattttcaaaacaattgtcgttgtggatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT