Sequence
atgc intronic sequence ATGC exonic sequence...tcactattcttttggcaacaaggttcacttgcagcatagaatggtacagaatagaatgatttgaattacttaaacttatttattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT
Basic information
species | Glycine max |
transcript | GLYMA03G40000.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 15
--------------------tcactattcttttggcaacaaggttcact-tgcagcatagaatggtacagaatagaatgatttga---attacttaaacttatt-----tattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT----------------------------
||| || | | || | ||| | | || ||| | | || || |||| | || |||| || | | | | | |||||||| | ||||| |||||| ||| ||||| ||||||||||| ||||| ||||| |||||||| |||||||||
gtaagtgtacatggctgttatcattaacatatctcgaatttgcctcaatattttttattgaaggagagagtttacctcaattttattcataacttttgttttctaaaaatgccactgtgttaattgcagTTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACTGTAAGTCTAATCAGGTTCCAGTTGGAAA
upper sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g24460.2 (Oryza sativa), 3'ss of exon 15
--------------------tcactattcttttggcaacaaggttcact-tgcagcatagaatggtacagaatagaatgatttga---attacttaaacttatt-----tattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT
||| || | | || | ||| | | || ||| | | || || |||| | || |||| || | | | | | |||||||| | ||||| |||||| ||| ||||| ||||||||||| ||||| ||||| |||||||| |||||||||
gtaagtgtacatggctgttatcattaacatatctcgaatttgcctcaatattttttattgaaggagagagtttacctcaattttattcataacttttgttttctaaaaatgccactgtgttaattgcagTTTATGGTTAAGAAGGGCATTGTGTTGACACCTCATGCTGAGTACTGCCTTCCAGGCATTACGCGTGCAACT
upper sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 25
---tcactattcttttggcaacaaggt--tcacttgcagcatagaatggtacagaatagaatgatttgaattacttaaacttatttattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT
|| || | | | | || | | || |||| || || | || | || | | || || | ||| ||| |||| | ||| | ||||||| | || || || || | |||| |||| ||||||||||||||||| |||||||| || ||||| || |||
ctttcgctctcatcattgaaaagaagcagtcccttgaag-attcattgattttgactgta--gacttcc-tgactgaaaaatattc-ctctgtttcatattgcagTTCTTAGTGAAGAAAGGTCATGTTCTGACACCTCATGCTGATTACTGCCTTCCTGGGATAACTCGAGCTACTMapped 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|6724770|gb|AW309169.1|AW309169EST: TCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATT TTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTT
genomic: TCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATTgtatgtcctc ... ctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTT
EST:
gi|16996517|gb|BM085889.1|BM085889EST: TCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATT TTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTT
genomic: TCATGCTCGACCAAGATGGTTATTTATCAGAAACCAATGCAACTAACATTgtatgtcctc ... ctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagaatagaatgatttgaattacttaaacttatttattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT
cttatttattgccctt CT-rich tract
atagaatgatttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcactattcttttggcaacaaggttcacttgcagcatagaatggtacagaatagaatgatttgaattacttaaacttatttattgcccttctttctgcagTTTGTTGTTAAAAAGGGCCGTGTTTTGACCCCTCATGCTGATTACTGTCTTCCTGGCATTACTCGTGCAACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - cttttgg
- - - - - - - - - - - - -cacttgc
- - - - - - - - - - - - - - - - - - - - - - - - gaatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg