Sequence
atgc intronic sequence ATGC exonic sequence...tttgcaacatcatgatccagtcatgtgttgaaagaatccctaaaaataataaaatgtattgattccattgattaacattcatgtctatttgtttacacagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG
Basic information
species | Glycine max |
transcript | GLYMA03G34650.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G34650.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g47949.1 (Oryza sativa), 3'ss of exon 8
tttgcaacatcatgatccagtcatgtgttgaaagaatccctaaaaata-ataaaatgtattg-att--ccattgattaacattc-atgt-ctatt-tgtttacacagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG
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-------------------gtttggtttttatag---tcctgtgtgtacattgattgttttgtactgctcattgttcaattttttatgttctatcgtttttgtctagGTTCCATGTGATGTTACACTTTGGGCTACAATTGGAGGCCAGGACGTGGATCGTCTTCCATCTGCTTCCACGTGCTATAACACACTCAAG
upper sequence: GLYMA03G34650.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G461948_T01 (Zea mays), 3'ss of exon 12
--tttgcaacatcatgatccagtcatgtgttgaaagaatccctaaaaataataaaatgtattgattccattgattaacattcatgtctatttgtttacacagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG
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tccgttcttggtttttctacagtgatatcaacttgagactcataatgtgctctaaatttgtttatgcaa--gaacgataattaacgttgttacttgatgtagGTTCCATGTGATGTAACACTTTGGGCATCAATTGGAGGCCAAGATGTAGATCGTCTTCCATCTGCTTCCACATGCTACAATACGCTCAAG
upper sequence: GLYMA03G34650.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G53090.1 (Arabidopsis thaliana), 3'ss of exon 12
tttgcaacatcatgatccagtcatgtgttgaaagaatccctaaaaataataaaatgtattgattccattgattaacattcatgtctatttgtttac-acagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG
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------gtttgtttttgaacttaagcttagaaatgtatgtttgatattct---gtttggtaattttgttttcttacttttgtgctttttcatcttctgcagGTCTCTTGTGATACCTCTCTTTGGGCTGCTATTGGAGGACAAGATGTAGAAAGACTTCCATCTGCTTCTACGTGCTACAATACTCTTAAG
upper sequence: GLYMA03G34650.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv08s0007g04290.t01 (Vitis vinifera), 3'ss of exon 12
tttgcaacatcatgatccagtcatgtgttgaaagaatccctaaaaataataaaatgtattgattccattgattaaca--ttcatgtctatttgtttacacagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG
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tttttcatcccgcattgcctttttgcccc-aaaaaatggggaaaagaaatattgatcctagcaggaaatgagaactgagttcagattt-tcactttctatagGTTGCATGCGATGTGCCTCTTTGGGCAACAATTGGGGGACAGGATGTAGAGCGACTTCCCTCAGCTTCCACATGCTACAACACGCTCAAGMapped 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|51344285|gb|CO985018.1|CO985018EST: CTCCATTACTTGGGTTCAAATACTTGCAGCCACCTTTTACCATCCACAAG GTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGAT
genomic: CTCCATTACTTGGGTTCAAATACTTGCAGCCACCTTTTACCATCCACAAGgtattcttga ... gtttacacagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataataaaatgtattgattccattgattaacattcatgtctatttgtttacacagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG
gattaac putative branch site (score: 2)
tttgttt putative PPT
aaaatgtattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcaacatcatgatccagtcatgtgttgaaagaatccctaaaaataataaaatgtattgattccattgattaacattcatgtctatttgtttacacagGTTGCATGTGATGTTCCTCTTTGGGCAACAATTGGAGGACAAGATGTAGATCGACTTCCATCAGCTTCAACCTGCTACAATACTCTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- tgcaaca
- - - - - catgatc
- - - - - - - - - - tcatgtg
- - - - - - - - - - - - - - - - - - -ccctaaa
- - - - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtc