Sequence
atgc intronic sequence ATGC exonic sequence...tttctgtgaagctaatggtgtgcattgggttgtgctgatacaccttctgccttttcttttcactttcaattattcaaaacaatttctttcttaactgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATA
Basic information
species | Glycine max |
transcript | GLYMA07G07850.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G07850.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g58750.2 (Oryza sativa), 3'ss of exon 3
tttctgtgaagctaatggtgtgcattgggttgtgctgatacaccttctgccttttcttt----tca-ctttcaattattcaaaacaatttctttcttaactgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATA--
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-atttgttgacgcaactttttg--tttgattacccatatatttttgtggtaaattctctaagatcatctaataatccttttggtggaaacaactat--gcttcagGAAGAAGCTAAATCAGTTGGACAACTTCGGAGC-AAAGGTTAGCAA-TTTGCTTGGCTGTTGCTGCGAAGGTGACGAGAGATTGCTTGTTGCAGAATACATG
upper sequence: GLYMA07G07850.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 3
tttctgtgaagctaatggtgtgcattgggttgtgctgatacaccttctgccttttcttttcactttcaattattcaaaacaatttctttcttaac--------tgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATA
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----tgcatagg-attgaattttatttgctt-tacc--cacaagtgcaaattttctaggacatggtcaaacactcaaaatgaccttttgtgaaatacgtaatttgtagGAAGAAGCTAGATCAGTTGGCCTGCTCCGAAGCAAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGCGATGAGAGATTGCTTGTTGCAGAATACA
upper sequence: GLYMA07G07850.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G055561_T01 (Zea mays), 3'ss of exon 4
---tttctgtgaagctaat-ggtgtgcattgggttgtgctgatacaccttctgccttttcttttcactttcaattattcaaaacaatttctttcttaactgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATA
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tcttttttgtgtatatgattggattttatttgcttgccccgaaag---tgcaaattttctaagacatggtcaaacaatcaatctggccttttgatttg-tgcagGAAGAAGCTAGATCAGTTGGCCTGCTCCGAAGCAAAAGGTTGGCAAATTTGCTTGGCTGTTGCTGCGAAGGTGATGAAAGGTTGCTTGTTGCAGAATACA
upper sequence: GLYMA07G07850.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01740.1 (Arabidopsis thaliana), 3'ss of exon 3
tttctgtgaagctaatggtgtgcattgggttgtgctgatacaccttctgccttttcttttcactttcaattattcaaaacaatttctttcttaactgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATA
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-----------------gtatggcatgtacctttcagtttatctagttgccaattctcaaatctattaact--ttggatatgtctgtttc-------cagGAAGAAGCAAGATTGGTTGGTCAGCTACGCAGCAAAAGAATGGCCAATTTACTCGGTTATTGCTGTGAAGGCGGCGAGAGGTTACTTGTGGCTGAGTTTA
upper sequence: GLYMA07G07850.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02900.t01 (Vitis vinifera), 3'ss of exon 3
tttctgtgaagctaatggtgtgcattgggttgtgctgatacaccttctgccttttcttttcactttcaattattcaaaacaatttctttctt--aactgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATA
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atattttgca--taaaggtccatcctaattttcgctgtccttcttcacaaaagttccaaaccttatgactgaactttgacagtttttcctttgcaaccttagGAAGAAGCAAGAGCAGTTGGTCAGCTCCGCAACCATAGATTGGCAAATTTGCTTGGTTGTTGTTGTGAGGATAATGAAAGGTTGCTGGTGGCGGAATATAMapped 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|16106128|gb|BI893868.1|BI893868EST: CTGTTAAGCGGTTTAATAGGAATGCTTGGCCAGATGCTCGGCAGTTTTTG GAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTG
genomic: CTGTTAAGCGGTTTAATAGGAATGCTTGGCCAGATGCTCGGCAGTTTTTGgtaaattcac ... ttaactgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgccttttcttttcactttcaattattcaaaacaatttctttcttaactgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATA
tcttaac putative branch site (score: 2)
tttctttcttaact CT-rich tract
aattattcaaaacaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctgtgaagctaatggtgtgcattgggttgtgctgatacaccttctgccttttcttttcactttcaattattcaaaacaatttctttcttaactgcagGAGGAAGCAAGATCAGTTGGTCAGCTTCGTAACCAAAGGTTGGCAAATTTGCTTGGTTGTTGCTGTGAAGGAGAGGAGAGGTTGCTTGTGGCAGAATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
-ttctgtg
- - - - - - - -tggtgtg
- - - - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - ctgatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaa