Sequence
atgc intronic sequence ATGC exonic sequenceGCAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAGTCTGATTTCATGATGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAGgtatgattataacttgtttagtttaagttagaaatctacatgttctgttccatcgagaaagtttttgtttgcaattatatttttgtgacaaatctacatt...
Basic information
species | Glycine max |
transcript | GLYMA16G09430.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G09430.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os11g23790.2 (Oryza sativa), 5'ss of exon 2
GCAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAGTCTGATTTCATGATGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAGgtatgattataacttgttt---agttt---aagttagaaatctacatgttc----tgttccatcgagaaagtttttgtttgcaattatatttttgt-gacaaatctacatt
|||||||| ||||| || ||||||||||||||||| |||| || | ||||| ||||| |||||||| |||||||| ||||| || || || ||||| | |||| ||| | ||| || | || || || ||| | ||| | || || | || ||| | || ||||| ||
TCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCTTTCTAATGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaaaactaatttcacattttgccaaaattgatgtcaactcattcataattttcaaaggatgaatatgttaactgctctcctagctttgttgat-----------
upper sequence: GLYMA16G09430.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G079452_T02 (Zea mays), 5'ss of exon 2
GCAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAGTCTGATTTCATGATGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAGgta--tgattataacttgtttagtttaagttagaaatctacatgttctgttccatcgagaaagtttttgtttgcaattatatttttgtgacaaatctacatt--
|||||||||||||| ||||| || |||||||||||||| | ||| | ||||| ||||| |||||||| || ||||| |||| ||| |||||| ||||| || | | | ||| || | | | | || || | | | | | || | | ||| | | | |||| | |
ACAAGGAGTTATTGGGAAGAGGGTGGATGAGATGGAGTCAGGTTTTCTTATGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggtagtca-ttgcctaactcca-ccaagtacctgtttgcataacagctt--atttattcttcactaggcgttaccactcatttgcctatctttactaa
upper sequence: GLYMA16G09430.1 (Glycine max), 5'ss of exon 2
lower sequence: AT5G48470.1 (Arabidopsis thaliana), 5'ss of exon 2
GCAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAGTCTGATTTCATGATGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAGgta---tgattataacttgtttagtttaagttagaaatctacatgttctgttccatcgagaaagtttttgtttgcaattatatttttgtgacaaatctacatt
||||||||||| || || || |||||||| ||||| || | || |||||||| ||||| ||||||||||| ||||| || || ||||| || || |||||| ||| | || | | || || | | | || | | | || || | | || | | | | | | |
ACAAGGAGTTATAGGGAAAAGGGTTGATGAAATGGAATCAGGGTTTATGATGGCTCTTGATTACATGATCCAACTTGCAGACAAAGACCAAGACGAGAAGgtaaaccaattctgcattttccctctgaatgtacacaaaaatatttctagaattgacttgagttttgctacatagaacgaccaggata-gctagaattgct--
upper sequence: GLYMA16G09430.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv00s0333g00020.t01 (Vitis vinifera), 5'ss of exon 2
GCAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAGTCTGATTTCATGATGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAGgtatgattataacttgtttagtttaagttagaaatctacatg-ttctgttccatcgagaaagtttttgtttgcaattat---atttttgtga-caaatctacatt
|||||||| ||||| |||||||||||| | |||||||| | || |||||||| || || |||||||| || ||||| || || ||||||||||||||||||| | | | | || | ||| | || | | ||| || | | | ||| ||| | | | |||||||| | |||| ||
ACAAGGAGTCATTGGGAAGAGAGTTGATCAAATGGAGTCGGGGTTTATGATGGCACTAGATTACATGATACAACTTGCTGAAAAGGACCAGGATGATAAGgtatttatttcaagttttcatttttattttggtgcttgcataattactctttgttaattcccatttgctttatattcctttcatttttgttatcaaaact-----Mapped 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|192298751|gb|FG991002.1|FG991002EST: TGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAG CGCAAGTCACTGTTGGAAGTTATCAAAGAGACAGTATTATCACATCTAACC
genomic: TGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAGgtatgattat ... ttggattcagCGCAAGTCACTGTTGGAAGTTATCAAAGAGACAGTATTATCACATCTAACC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAGTCTGATTTCATGATGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAGgtatgattataacttgtttagtttaagttagaaatctacatgttctgttccatcgagaaagtttttgtttgcaattatatttttgtgacaaatctacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG