Sequence
atgc intronic sequence ATGC exonic sequencegttagtagcatttgacacgtctttttagcttttcaccactcttttttgcatttgtcagatttattttgctttggtaaaaattgaaactttggacttttgtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
Basic information
species | Glycine max |
transcript | GLYMA03G27570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G27570.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
gttagtagcatttgacacgtctttttagcttttcaccactcttttttgcat-ttgtcagatttattttgctttggtaaaaattga--aactttggacttttgtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
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-----------gtgagctgcttaatcactgttatgccattgtttcttgtaggctcacagaattgttatataccattgcattttgcttaacttt---tccctgcactaccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC
upper sequence: GLYMA03G27570.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
----------------gttagtagcatttgacacgtctttttagcttttca---ccactcttttt--tgcatttgtcagatttattttgctttggtaaaa----attgaaactttggacttttgtttgtt--tagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
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gttagtttccctctcttttctttgtgtgt-atattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcgg-ttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC
upper sequence: GLYMA03G27570.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagtagcatttgacacgtctttttagcttttcaccactcttttttgcatttgtcag---atttattttgctttggtaaaaattgaaactttggacttttgtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
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--aaatatc-tccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctg-ttggcttacgaccaatgttgtaaaattt-------gcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAACMapped 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|192331838|gb|FK024942.1|FK024942EST: TGAAACCTGTAACAGGTGTCAGCCGAGTGACGGTCAAGAAGAGCAAGAAT ATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGAC
genomic: TGAAACCTGTAACAGGTGTCAGCCGAGTGACGGTCAAGAAGAGCAAGAATgttagtagca ... gtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGAC
EST:
gi|7146353|gb|AW508275.1|AW508275EST: TGAAACCTGTAACAGGTGTCAGCCGAGTGACGGTCAAGAAGAGCAAGAAT ATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGAC
genomic: TGAAACCTGTAACAGGTGTCAGCCGAGTGACGGTCAAGAAGAGCAAGAATgttagtagca ... gtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcagatttattttgctttggtaaaaattgaaactttggacttttgtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
cttttgttt CT-rich tract
taaaaattgaaacttt 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
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gttagtagcatttgacacgtctttttagcttttcaccactcttttttgcatttgtcagatttattttgctttggtaaaaattgaaactttggacttttgtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA