Sequence
atgc intronic sequence ATGC exonic sequence...cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttattatgttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
Basic information
species | Glycine max |
transcript | GLYMA20G28950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g10410.1 (Oryza sativa), 3'ss of exon 3
----------------------------------cttttcctgcttaacagtagttggg---gctcatgtga-------tccagatataactggacaacttattatgttctttctgacattatttcgttgccaaaat-------------ttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
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gtaattgaagtcacaaattgttctttcacttgtctttcttgggattaccagttattcagattgattgtgtgaagaacgttccgcctgcatctctgccctatacgttatccgattgtacaaacctatgcatctgaaataatgatcctttttccatcagGATCGCATTATTGCTCGACTGCAACAACCTTACTCCCTCGATTGCATTCCTGTTGAAGCTGAATACCAG
upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 3
----------------------------------------cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttat-tatgttctttctgac--attattt------cgttgccaaaatt------------tggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
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gtaatataagccacatacctgcattgtattattcttgcttcctttcttgagtttcaa-ggttatatgttgttttagtcagatgtgtcaagagcagttacatatgcattagccagttgatcacttgatctacgtgtctaaaattgtgtctattgtctatcagGATCGTATTATTGCTCGGCTGCAACAGCCTTATTCCCTTGACTGCATACCAGTTGAAGCTGAATACCAG
upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 3
-cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttattat-gttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
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acattagcttctgagtacgtcttaagactgccttatcttttagtcaatttgtgaccctctagttgaagtttattacatcatttgtctgttt--atataacagGATCGCATCATTGCTCGTCTCCAACAACCTTATTCGCTAGATTGCATTCCAGTTGAAGCAGAATATCAG
upper sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 3
cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttat--tatgttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
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-tttcttcatatacatacacatgcatcttcagc-acacaggtaaaatgacatcattaatcctgtgtaacatatatgcgggaatctttgttccattttggcagGATCGCATTATAGCTCGTCTTCAACAACCATATTCACTAGATTGCATTCCAGTGGAAGCAGAATTTCAGMapped 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|208024965|gb|GD822411.1|GD822411EST: AAGATGTTATTCAGAACAAG GATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCT
genomic: AAGATGTTATTCAGAACAAGgtaatgtaat ... aatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actggacaacttattatgttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
ttctgac putative branch site (score: 2)
ttattatgttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttcctgcttaacagtagttggggctcatgtgatccagatataactggacaacttattatgttctttctgacattatttcgttgccaaaatttggcagGATCGCATTATAGCTCGCCTACAGCAGCCGTATTCCCTTGATTGCATTCCTGTTGAAGCAGAATATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - tcctgct
- - - - - - - - - -gttgggg
- - - - - - - - - - - - - -tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgcca