Sequence
atgc intronic sequence ATGC exonic sequencegtaattcactagttcttcttactgaaaatatatacaactgtttctacaaaaatctctgactttggttatcttttggtttgcaccagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 3
gtaattcactagttcttcttactgaaaatatatacaactgtttc-----tacaaaaatctctgactttg-gttatcttttggtttgcac--------cagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT
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atagggttttatttcttattaattataattcatctagttgtttctaatttatatttattgttagtttcatataattgattgatgcacatacttttcgcagTGTAATTGTGGAAGCTCTGAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
--gtaattcactagttcttcttactgaaaatatatacaactgtttctacaaaaatctctgactttggttatctt---ttggtttgcac----------cagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT
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aaagaagattttatttcttattaatcataatccatctacttgtttcta-atttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
upper sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
---------gtaattcactagttcttcttactgaaaatat--atacaac---tgtttctacaaaaatctctgactttggttatcttttggtttgcac-cagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT
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tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttatgtcagt-tctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTTMapped 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|124761433|gb|EH851563.1|EH851563EST: GATGGGAACGATGATGATCAGCCTGAGCGAAAACGCCCTGCTTTTGCTAG TGTGATTGTTGAGGCT
genomic: GATGGGAACGATGATGATCAGCCTGAGCGAAAACGCCCTGCTTTTGCTAGgtaattcact ... tttgcaccagTGTGATTGTTGAGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacaactgtttctacaaaaatctctgactttggttatcttttggtttgcaccagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT
ctctgac putative branch site (score: 3)
tacaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcactagttcttcttactgaaaatatatacaactgtttctacaaaaatctctgactttggttatcttttggtttgcaccagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC