Sequence
atgc intronic sequence ATGC exonic sequence...aattattagttagacgacatttagaaatttcttctgaaattctggacttaacttttaatttcataatgtgctttgtgttgttttttcctctatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG
Basic information
species | Glycine max |
transcript | GLYMA14G29810.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 14
aattattagttagacgacatttagaaatttcttctgaaattctggacttaacttttaatttcataatgtgctttgtg-ttgttttttcctctatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG
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-----------------------gtgattacttc--aactgttgggatttgttttgtgtgtta-gacatgttaaatggctcatctaacttcgactctacagGTATCGAACTGTGGGATGAGTGATGCTATCGGTCCTGTGCATGTGAAAGAACGACCAAGCATAGAGATGCAATCAAGGATAGATGCTGAG
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 14
aattattagttagacgacatttagaaatttcttctgaaattctggacttaacttttaatttcataatgtgctttgtgttgttttttcctctatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG
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-----------------------gtaattacttcgtctgttgggaaat--attttgtatta---gacgtgttaaatggtcatctaactatgactctacagGTATCAAACTGTGGGATGAGTGATGCTATCGGTCCTGTGCATGTGAAAGAGCGACCAAGTGTAGAGATGCAATCAAGGATAGATGCTGAG
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 14
------------------------------------------------------------------aattattagtt-----agacgacattt-agaaattt--cttctgaaattct------ggacttaacttttaatttcataatgtg-------ctttgtgttgt-------------tttttcctctatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG
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gtaacctcatgtacatgtgcttaattgcttctttttttctggtttatcaaaagagttagcctttggttcttttagttttctggaatgaggtttgagggacttagtctctgagatccttaaggtgaacttacaagttaatgcgagaagatggatcttacctcttgttgtagttgtagtaatgcttttctttttaatggaagGTATCGAGTTGTGGGATGAGTGAGGCAATAGGACCAGTTCATATAAAAGAAAGACCAAGCTCTGATATGCAATCACGCATTGATGCCGAG
upper sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 14
aattattagttagacgacatttagaaatttctt----ctgaaat-tctggacttaacttttaatttcataatgtgctttgtgttgttttt--tcctctatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG
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-----ccaa--acatagccttaaggaatagctgatggctgaaacctcttaataagagctttcttcatttatttctcttaatgctgagagcaaccctttctatgcaagGTATCTACTTGCGGGATGAGTGATACAATTGGGCCAATTTATATCAAAGATCGACCAGGTGTAGAAATGGAATCGCGAATTGATGCGGAAMapped 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|7692496|gb|AW760601.1|AW760601EST: CTGGAGCAAGTAGTGATCTCCACACTGCTACTGAGCTTGCCCAATACATG GTATCGAATTGTGGGATGAGTGATGCCATCGGGCCAGTT
genomic: CTGGAGCAAGTAGTGATCTCCACACTGCTACTGAGCTTGCCCAATACATGgtaattttct ... tatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttaacttttaatttcataatgtgctttgtgttgttttttcctctatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG
ttttaat putative branch site (score: 3)
ctttgtgttgtttttt putative PPT
acttttaatttcataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattattagttagacgacatttagaaatttcttctgaaattctggacttaacttttaatttcataatgtgctttgtgttgttttttcctctatgcacaagGTATCGAATTGTGGGATGAGTGATGCAATCGGGCCAGTTAATATAAAAGAGCGACCAAGTTCTGAAATGCAGTCACGTATTGATGCAGAG
- - - - - - - - - - - - - - -tcttctg
- - - - - - - - - - - - - - - - - - - attctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctttg