Sequence
atgc intronic sequence ATGC exonic sequence...tcttctttttttttttttgctttattctttcactctaccaaatgtagggactatcatttattagaatcattcaatggttacttactctatcttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTCTTCCTTGGTGGAGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
Basic information
species | Glycine max |
transcript | GLYMA08G03550.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 16
-----tcttctttttttttttttgctttattctttcactctaccaaatgtagggactatcatttattagaatcattcaatggttacttactctatcttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTCTTCCTTGGTGGAGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
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agaattgattatatcttggaataaaattattaaatgaatgtcatgtttgatagtgttgtgatgc-ttggaatta----acatctgcctacttcataaatctttagGTGACTGCAACTCCTGATCTTATGCTGGGCTATTTAGATTTCTTCCTTGGGGGAGATGAAAAAAGGCCTGATCTTCCACCTCGTCTTCGCCAAAGGTTTC
upper sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G350818_T01 (Zea mays), 3'ss of exon 9
---tcttctttttttttttttgctttattctttcactctaccaaatgtagggactatcatttattagaatcattcaatggttacttact-ctatcttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTCTTCCTTGGTGGAGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
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tagtatcggaaagcataggttgcgttactcttgcaattgtttacaggt--gaattgtcttgtcatatataggattgatggtttctgatttccaaatta--atagGTAGCTGCTACTCCAGATTTAATGCTGGGTTATTTAGATTTCTTCCTTGGTGGGGATGAGAAAAGGACTGATCTTCCTCCTCGGCTTCATCAAAGGTTTC
upper sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 6
tcttctttttttttttttgctttattctt-tcactctaccaaatgtagggactatcatttattaga--atcattcaatggttacttactctatcttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTCTTCCTTGGTGGAGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
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--ttgatcaactgtatactgtttatgctcattattgtttccgaagctggaa-tagtacctttcagcctgtcatttatttaatttctgcttttgcaatgtctagGTGACTGCAACCCCAGATCTAATGCTAGGGTATTTAGATTTCTTCCTTGGGGGAGATGAAAAAAGGCCTGATCTTCCACCTCGTCTTCGTCAAAGGTTTC
upper sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G820781_T01 (Zea mays), 3'ss of exon 1
tcttctttttttttttttgctt-tattctttcactctaccaaatgtagggactatcatttattaga--atcattcaatggttacttactctatcttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTCTTCCTTGGTGGAGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
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-ttggtcaattgtatactgtttatgttcattcttgtttccaaagat--ggaatattatcttccagcctatcatttatttgatttctgcttttgcaatctctagGTGACTGCAACCCCAGATTTAATGCTAGGGTATTTAGATTTCTTCCTTGGGGGAGATGAAAAGAGGCCTGATCTTCCACCTCGTCTTCGTCAAAGGTTTCMapped 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|207790020|gb|GD762641.1|GD762641EST: ATGCATGCTTGCGTTCTTGCCGTTCACGAGCACTTTATGAAGGGCTGAAG GTAGGTGCAACATCTGATCTGATGCTGGCATATCTGGATTTC
genomic: ATGCATGCTTGCGTTCTTGCCGTTCACGAGCACTTTATGAAGGGCTGAAGgtacttaaga ... cttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTC
EST:
gi|207800583|gb|GD772816.1|GD772816EST: ATGCATGCTTGCGTTCTTGCCGTTCACGAGCACTTTATGAAGGGCTGAAG GTAGGTGCAACATCTGATCTGATGCTGGCATATCTGGATTTC
genomic: ATGCATGCTTGCGTTCTTGCCGTTCACGAGCACTTTATGAAGGGCTGAAGgtacttaaga ... cttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agggactatcatttattagaatcattcaatggttacttactctatcttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTCTTCCTTGGTGGAGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
tacttac putative branch site (score: 1)
ctctatctt CT-rich tract
tatcatttattagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttctttttttttttttgctttattctttcactctaccaaatgtagggactatcatttattagaatcattcaatggttacttactctatcttgctacagGTAGGTGCAACATCTGATCTGATGCTAGCATATCTGGATTTCTTCCTTGGTGGAGATGAGAAAAGACCTGATCTGCCTCCTCGTCTTTATCAAAGATTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - -tgcttta
- - - - - - - - - - - - - ctttcac
- - - - - - - - - - - - - - - - - ctaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcaa