Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttgaaatctttaaagcttatttctgttggctttgtagttctgattgcacattatgttgtggactttttacgggttgacagTACCTTGTCTACGGAGAGCTGCTTCTGTGGCAGAGGATTATGAAGCTGCTGGAGGTGAAGTGTTGGTTGATGATGAAGATAATGATGGTTGGCTGGCTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61500.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G36540.1 (Glycine max), 3'ss of exon 2
------------------------------------gtaaatttgaaatctt----taaagcttatttctgttggctttgtagttctgattgcacattatgtt---gtggactttttacggg-ttgacagTACCTTGTCTACGGAGAGCTGCTTCTGTGGCAGAGGATTATGAAGCTGCTGGAGGTGAAGTGTTGGTTGATGATGAAGATAATGATGGTTGGCTGGCTAC
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gtatgattgagatctgagtatgcctttacatcatgcgtgtttttttcttcttctcctaaaagcaagcagtaatatctgagaatttcctgttctgtttcatggtcatgctgatttttggagtacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAAGAATATGAAGCTGCTGGAGGGGAAGTTTTACTAGATGATGAAGATAATGATGGCTGGCTAGCAAC
upper sequence: AT5G61500.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G00830.3 (Glycine max), 3'ss of exon 2
-------------------------------------------gtaaatttgaaatctttaaagc------ttatttctgttggctttgtagttc-tgattgcacattatgttgtggactttttacgggttgacagTACCTTGTCTACGGAGAGCTGCTTCTGTGGCAGAGGATTATGAAGCTGCTGGAGGTGAAGTGTTGGTTGATGATGAAGATAATGATGGTTGGCTGGCTAC
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gtatgatcaagatctgagtatgcctttacatcatgcgtgttctttgtttttcctctcataaaagcaaccagtaagatctgagaatgtcctgtttcatggtcatgc-tgatttttggagttgcttcatacttaacagTGCCTTGTCTTCGGAGAGCTGCATCTGTTGAAGAGGAATATGAAGCTGCTGGAGGGGAAGTTCTACTCGATGATGAAGATAATGATGGCTGGCTAGCAACMapped 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|125250566|gb|EL264651.1|EL264651EST: TTTTTGATTACTAGAAATG TACCTTGTCTACGGAGAGCTGCTTCTGTGGCAGAGGATTATGAAGCTGCTG
genomic: TTTTTGATTACTAGAAATGgtaaatttga ... gggttgacagTACCTTGTCTACGGAGAGCTGCTTCTGTGGCAGAGGATTATGAAGCTGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggctttgtagttctgattgcacattatgttgtggactttttacgggttgacagTACCTTGTCTACGGAGAGCTGCTTCTGTGGCAGAGGATTATGAAGCTGCTGGAGGTGAAGTGTTGGTTGATGATGAAGATAATGATGGTTGGCTGGCTAC
ttctgat putative branch site (score: 3)
attatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatttgaaatctttaaagcttatttctgttggctttgtagttctgattgcacattatgttgtggactttttacgggttgacagTACCTTGTCTACGGAGAGCTGCTTCTGTGGCAGAGGATTATGAAGCTGCTGGAGGTGAAGTGTTGGTTGATGATGAAGATAATGATGGTTGGCTGGCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA