Sequence
atgc intronic sequence ATGC exonic sequencegtaatcaccattactatttcgttattacatagaagatgatgttttcttttccttctttttaattatgtaatttattgactgatttatgtgctttttgtttttggtttttttttttcggttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA01G00780.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G00780.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g10850.1 (Oryza sativa), 3'ss of exon 2
gtaatcaccattactatttcgttattacatagaagatgatgttttcttttccttctttttaattatgtaatttattgactgatttatgtgctttttgtttttggtttttttttttcggttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
|| |||| | || | || | | | | || | | | | | | || || || | || | | ||| | ||| ||||||| ||||| |||||| ||||||||| ||||||||||| |||||| ||||| ||||| || ||||| | ||||||||||| ||||| | ||||
--------------------cccatgccatacat--tgctattctaagcgctgttctgctaggtttctgagtagactatattttcatatgtcctaagtcccaa---tccatacttctgctttc---agCTTAAAGAGCTTGAGAAGTTGGGTCCCAAAAAGGGTGTCATCAGTCAGTCAGTGAAGGATGTTGTGCAAAGCCTGGTGGATGATGATCTTGTCTTGAAAG
upper sequence: GLYMA01G00780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G102242_T02 (Zea mays), 3'ss of exon 2
gtaatcaccattactatttcgttattacatagaagatgatgttttcttttcc-ttctttttaattatgtaatttattgactgatttatgtgctttttgtttttggtttttttttttcggttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
||| || | | | ||| |||| || | || ||| || || || ||| | | || || | | | ||| |||||||||||||| ||||| |||||||| | ||||| || ||| ||||||||||||||||||||| ||||| | ||||||||||| ||||| | || |
-----------------------------cagattttgctactgtagcttctgttctgttaagttttgtcatgtaggatgtgtttttccgatgccatagaatataattcttaccatatgctatttttagCTTAAGGAGCTAGAGAAAATGGGTCCTAAAAAGGGAGTGATTAGTCAGTCTGTGAAAGATGTGGTGCAAAGCCTGGTGGATGATGATCTTGTCTTGAAGG
upper sequence: GLYMA01G00780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G29170.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------gtaatcaccatta-ctatttcgttattacatagaagatgatgttttcttttccttctttttaattatgtaatttattgact----gatttatgtgctttttgtttttggtttttttttttcg---gttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
|| | | ||| ||| || || ||| | || | | || ||| | ||| | | ||| | ||| || || ||| | | | ||| | || |||| ||||| || ||||||||||| || | ||||||||| ||| |||||||||||||||||| |||| |||||||| |||||||| |||||| | ||||
gtgagcactttctttagtttttacaacttgctaatttttggacgcctttgaactagctttatctaccaagtgatctgatatctagagtcgtgaagtgcatatactgcctaaatttgttgctattgaacttttgggtttgtgatacaagcacttatgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG
upper sequence: GLYMA01G00780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g02770.t01 (Vitis vinifera), 3'ss of exon 1
gtaatcaccattactatttcgttattacatagaagatgatgttttcttttccttctttttaattatgtaatttattgactgatttatgtgctttttgtttt-tggtttttttttttcggttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
| |||| | | | || | ||||| | || || || || | || || | | ||| | | | |||| | | || |||| ||||| || |||||| ||||||||| ||||||||| || ||||||||||||||||| ||||||||| |||| || |||||||||||| | ||||
-----------------------agcccatatcatac-agacttggatggccttc-----aggaattaaaagtactgttttcttagtgagaataatgtatcactgatacgttttgcctatgaatttcagCTCAAGGAACTTGAGAAGTTGGGTCCCAAGAAGGGTGTTATCAGCCAGTCTGTGAAAGATGTTGTCCAAAGTCTAGTCGACGATGACCTTGTTGCAAAAG
upper sequence: GLYMA01G00780.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S41_172V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaatcaccattactatttcgttattacatagaagatgatgttttcttttccttctttttaattatgtaatttattgactgatttatgtgctttttgtttttggtttttttttttcggttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
|| | | | |||| | || ||| || | |||| |||| | | | | | ||| | |||| || || || ||| | |||| || || || |||||| | || || | ||| || || || ||| || || ||||||||||| || || |||||||||||||| ||||||| |||||
------------tgtactcctcggtatggtagaggcgaatctttaagattttcttcagccaatt-tgtaggtgaaacattactgaatgc--------taactggtgttctt-----ggcttt--gaagCTGAAAGATCTGGAGAAGCTTGGACCTAAGAAAGGGGTTATAAGTCAATCAGTCAAAGATGTGGTGCAGAGCTTAGTGGATGATGATCTTGTTTTCAAAGMapped 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|298178062|gb|HO027445.1|HO027445EST: AGCGCGAGAAGATGCTTCAAATCTTTTACGAGTCGCAAGACTTCTACCTG CTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCT
genomic: AGCGCGAGAAGATGCTTCAAATCTTTTACGAGTCGCAAGACTTCTACCTGgtaatcacca ... ttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCT
EST:
gi|33390430|gb|CA853625.1|CA853625EST: AGCGCGAGAAGATGCTTCAAATCTTTTACGAGTCGCAAGACTTCTACCTG CTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCT
genomic: AGCGCGAGAAGATGCTTCAAATCTTTTACGAGTCGCAAGACTTCTACCTGgtaatcacca ... ttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgactgatttatgtgctttttgtttttggtttttttttttcggttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
ctttttgtttttggtt CT-rich tract
tttttgtttttggttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcaccattactatttcgttattacatagaagatgatgttttcttttccttctttttaattatgtaatttattgactgatttatgtgctttttgtttttggtttttttttttcggttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA