Sequence
atgc intronic sequence ATGC exonic sequencegtgattgattgaccatttgagtttctcacatttgcttttctatggtatagagtatatattctgtcttgagtgttaatgaatcttttgtgcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCTGAGGATGCATTATCACAAG
Basic information
species | Glycine max |
transcript | GLYMA10G42280.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G42280.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g41640.1 (Oryza sativa), 3'ss of exon 1
-------gtgattgattgaccatttgagtttctcacatttgcttt-tctatggtatagagtatatattctgtcttgagtgttaatga----atcttttgtgcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCTGAGGATGCATTATCACAAG
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gtttgacacgagtgatcacccacccaattcagtaacaagcaaagaatctgaagctaccattgactgctat-tgttgaatgatgatgatgatgttgtttgtgcagGTACTTGAGAGCCATCTTGAGCCGCTGACGAATCAGCAGTTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCACAGG
upper sequence: GLYMA10G42280.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g15480.2 (Oryza sativa), 3'ss of exon 7
--------gtgattgattgaccatttgagtttctcacatttgcttttctatggtatagagtatatattctgtcttgagtgttaatga-atcttttgtgcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCTGAGGATGCATTATCACAAG
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gttttgacacgatcgagtgatcacccacccaattcag--caacaagcaaagaatctgaagc-taccattgaccgccattgttgatgatgttgtttgtgcagGTTCTTGCCAGCCATCTTGAGCCGCTGACGGATCAGCAGCTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCGCAGG
upper sequence: GLYMA10G42280.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g03230.t01 (Vitis vinifera), 3'ss of exon 9
--------gtgattgattgaccat-----ttgagtttctcacatttgctttt-ctatggt--atagagtatatattctgtcttg-------------agtgttaatgaatcttttgtg---cagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCTGAGGATGCATTATCACAAG
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gtaatttgaagatttattgcttttagaccttgaatcttttttatccagttctgcaatggctgaaggaatgtatagtttttttggttgattcacatctatttctattttatttttggagtttcagATACTTGGGAACCAACTTGAACCTTTAACAGATCAGCAGCTGATGGGCATATGTAATCTACAACAGTCCTCACAGCAAGCTGAGGATGCATTATCACAAGMapped 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|51335709|gb|CO979575.1|CO979575EST: AAAGATGCTTCATATGGCTCGGTGGTTTTCGATCTTCGGAACTTCTCAAG ATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATT
genomic: AAAGATGCTTCATATGGCTCGGTGGTTTTCGATCTTCGGAACTTCTCAAGgtgattgatt ... ttttgtgcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatggtatagagtatatattctgtcttgagtgttaatgaatcttttgtgcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCTGAGGATGCATTATCACAAG
tgttaat putative branch site (score: 3)
tcttttgt putative PPT
tatagagtatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattgattgaccatttgagtttctcacatttgcttttctatggtatagagtatatattctgtcttgagtgttaatgaatcttttgtgcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCTGAGGATGCATTATCACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG