Sequence
atgc intronic sequence ATGC exonic sequencegtatttacttgttcatatgttatatatttctttgattctgttagttatttgtggtttgaattatcttcacaaattcataatgtttctaatgttttcatagGAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTGTAAAGCAGCTCTTGATTGATGGAACCTTAGCTGGATGTGCTTTGGATGG
Basic information
species | Glycine max |
transcript | GLYMA09G39090.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 1
------------------------gtatttacttgttcatatgttatatatttctttgattctgttagttat--ttgtggtttgaattatcttcacaaattcataatgtttctaatgttttcatagGAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTGTAAAGCAGCTCTTGATTGATGGAACCTTAGCTGGATGTGCTTTGGATGG
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gtaaggtttatcttcaacccctttctttcttctgctttatgcattatatattccga-aataatgcttatcatgcctttagttcagccgtaaaacacag---tataattttcttgtttatctcacagGAGCATTCATAGTAAATACTGGAAGTTGCCAACTTATAGATGATTGTGCACTCAAACAGCTATTGATTGATGGTACAATAGCTGGTTGTGCATTGGATGG
upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G476107_T02 (Zea mays), 3'ss of exon 3
----------------------------gtatttacttgt--tcatatgttatatat-ttctttgattctgttagttatttgtggtttgaattatcttcacaaatt-------cataatgtt-tctaatgttttca------tagGAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTGTAAAGCAGCTCTTGATTGATGGAACCTTAGCTGGATGTGCTTTGGATGG
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gtatgcttttcttttataattgtgttatgttgcttcttgtagtctgaaatagtgcatgtccttcctttattttagttctatatcatcttttttttgaccggaaagttctatatcatcttgtcatcgaatattttgaatcctgcagGAGCTTTCATAGTCAATACTGGTAGTTGCCAGCTTATAGATGACTGTGCTCTCAAACAGCTCTTGATTGATGGTACCATAGCTGGTTGCGCATTGGATGG
upper sequence: GLYMA09G39090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 2
gtatttacttgttcatatgttatatatttctttgattctgt-tagttatttgtggtttgaattatcttcacaaattcataatgtttctaatgttttcatagGAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTGTAAAGCAGCTCTTGATTGATGGAACCTTAGCTGGATGTGCTTTGGATGG
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gtatttttattttgacat---atactttctataaactttttacaagtccccctcccccctatttgctttaacagttaatca-gtttct----tctgtgcagGGGCATTTCTTGTGAATACGGGGAGCAGTCAGCTGCTGGATGATTGTGCTCTGAAGCAGCTGTTGATTGACGGCACCATTGCTGGCTGTGCTCTGGATGGMapped 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|151408973|gb|EV278781.1|EV278781EST: CATGTAAAACCTG GAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTG
genomic: CATGTAAAACCTGgtatttactt ... gttttcatagGAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTG
EST:
gi|8283239|gb|BE020800.1|BE020800EST: TGAAACAATGCAGATTATTAATGCTGAATGTCTTCAACATGTAAAACCTG GAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTG
genomic: TGAAACAATGCAGATTATTAATGCTGAATGTCTTCAACATGTAAAACCTGgtatttactt ... gttttcatagGAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgtggtttgaattatcttcacaaattcataatgtttctaatgttttcatagGAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTGTAAAGCAGCTCTTGATTGATGGAACCTTAGCTGGATGTGCTTTGGATGG
ttctaat putative branch site (score: 2)
tgttttc CT-rich tract
aaattcataatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttacttgttcatatgttatatatttctttgattctgttagttatttgtggtttgaattatcttcacaaattcataatgtttctaatgttttcatagGAGCTTTTATTGTAAATACGGGCAGTAGTCAACTTTTGGATGATTGTGCTGTAAAGCAGCTCTTGATTGATGGAACCTTAGCTGGATGTGCTTTGGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA