Sequence
atgc intronic sequence ATGC exonic sequence...gaatttaatggccgaaacttaacctattggtctctttcacataaaagacacacggatacactaaaaaacatactttgactgcatgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC
Basic information
species | Glycine max |
transcript | GLYMA12G07890.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 20
-----------------------------------------------------------------------------------------------gaatttaatggccgaaac--ttaacctattggtctctttcacataa----aagacacacggatacactaaaaaacatactttgactgcatgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC
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gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttatgag-gtggtggtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC
upper sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os12g01140.1 (Oryza sativa), 3'ss of exon 20
-----------------------------------------------------------------------------------------------gaatttaatggccgaaac--ttaacctattggtctctttcacataa----aagacacacggatacactaaaaaacatactttgactgcatgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC
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gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttacgag-gtggtggtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC
upper sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G001457_T01 (Zea mays), 3'ss of exon 1
gaatttaatggccgaaacttaacctattggtctctttcacataaaagacaca-cggatacactaaaaaacatactttgactgcatgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC
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-------------gtaact-aatcttgtgctaaaagaaacatgtatgatacagctactatatgatagtgagttctctttctac------tggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC
upper sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 21
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20
gaatttaatggccgaaacttaacctattggtctctttcacataa-aagacacacggataca-ctaaaaaacatacttt--gactg--catgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC
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------aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaatactgttttttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCCMapped 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|51337410|gb|CO981276.1|CO981276EST: AATTATAACGGGTTCAGGCCATACAAGTGCTGTGGATTGGTGGGCTCTTG GAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGA
genomic: AATTATAACGGGTTCAGGCCATACAAGTGCTGTGGATTGGTGGGCTCTTGgtaattcttt ... cttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGA
EST:
gi|151393210|gb|EV263085.1|EV263085EST: AATTATAACGGGTTCAGGCCATACAAGTGCTGTGGATTGGTGGGCTCTTG GAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGA
genomic: AATTATAACGGGTTCAGGCCATACAAGTGCTGTGGATTGGTGGGCTCTTGgtaattcttt ... cttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agacacacggatacactaaaaaacatactttgactgcatgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC
tgccttacttttttc CT-rich tract
taaaaaacatacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaatttaatggccgaaacttaacctattggtctctttcacataaaagacacacggatacactaaaaaacatactttgactgcatgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC