Sequence
atgc intronic sequence ATGC exonic sequence...actgaaatcctacattattgacatcaaccttttgagttaatcaattgaaatttatcattgttatgatctaatagtgtttgctttatctgggaccttgaagGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
Basic information
species | Glycine max |
transcript | GLYMA13G08160.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 7
actgaaatcctacattattgacatcaaccttttgagttaatcaatt----gaaatttatcattgttatgatctaatag--tgtttgctttatctgggaccttgaagGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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-----agacttactcaaagctcttttttttttctagttactcttttctccaacgttcatttccttcataagttcgtaccttactggagttaactttgtgcttta-gGCTATCGCTGGTGAAGCTGGTGTGCCATTTTTTTATCGGGCAGGTTCTGAATTTGAGGAAAT
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 7
actgaaatcctacattattgacatcaaccttttgagttaatcaattgaaat-ttatcattgttatgatctaatagtgtttgctttatctgggaccttga---agGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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----ggacgccattgtgccatctccagctgttatcctatagtttttgtgctattgctgttgtcttgaccaaacataccttactggagctgtctttttgccccagGCCATTGCTGGAGAAGCTGGTGTACCATTCTTTTACCGAGCAGGCTCTGAATTTGAGGAAAT
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 7
actgaaatcctacattattgacatcaaccttttgagttaatcaattgaaat-ttatcattgttatgatctaatagtgtttgctttatctgggaccttga---agGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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----atatgccattgtgccatctgcagctgttatcctatagtttttgtgctactgctgttgtcttgaccaaacataccttactggagctggctttttgctccagGCCATTGCTGGAGAAGCTGGCGTACCATTCTTTTACCGAGCAGGTTCTGAATTTGAGGAAAT
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------------------------------actgaaatcctacattattgacatca-accttttgagttaatcaattgaaatt----tatcattgttatgatcta----atagtgt-ttgctttatctgggaccttgaagGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccacttaataataaattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
upper sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 7
-----actgaaatc-ctacattattgacatcaaccttttgagttaatcaattgaaatttatcattgttatgatctaatagtgtttgctttatctgggaccttgaagGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
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tccgtattaatttctctgcccttttcatttttgtcttt-gatttaatcaat-gatattttttac-attctaatctatg---gtttgattcatttggaactttgaagGCTATTGCTGGAGAGGCTGGAGTACCATTTTTCTATAGAGCAGGTTCTGAATTTGAAGAAATMapped 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|193689513|gb|FK630996.1|FK630996EST: GGATTCTTTTGACAGGAGCACCTGGAACTGGAAAAACTCTGCTAGCCAAG GCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAA
genomic: GGATTCTTTTGACAGGAGCACCTGGAACTGGAAAAACTCTGCTAGCCAAGgtcagttagt ... gaccttgaagGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaatttatcattgttatgatctaatagtgtttgctttatctgggaccttgaagGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
atctaat putative branch site (score: 3)
tttatcattgttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgaaatcctacattattgacatcaaccttttgagttaatcaattgaaatttatcattgttatgatctaatagtgtttgctttatctgggaccttgaagGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - -tcctaca
- - - - - - - - - - - atcaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg