Sequence
atgc intronic sequence ATGC exonic sequencegtattgtgcttttatttttacttttttaagattttctgccttggtatttgtctctttatcatgttgatcaatgtgttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
Basic information
species | Glycine max |
transcript | GLYMA10G39670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G39670.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os09g21510.1 (Oryza sativa), 3'ss of exon 5
gtatt--gtgcttttatttttacttttttaagat---tttctgccttggtatttgtc-tctttatcatgttgatcaatgtg--ttgctggatat-agGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
||| | | ||| | | | || | | | || | |||| | | || ||| | || ||| ||| || |||| || |||||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||| |||| | | ||
gtactcaaaatctgaattctgaacacacaataatatgtatttattttaccacttgttgtgctcattatgattattcctgttatttgtcaaattccagGGAGCGAACATTCTTGTTGATAACAAAGGATGCATTAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: GLYMA10G39670.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G098828_T01 (Zea mays), 3'ss of exon 5
gtattgtgcttttatttttactttttta---agattttctgccttggtatttgtctc------tttatcatgttgatc---aatgtgttgctggatat-agGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
|||| || | | ||| | | | | |||| || |||||| | || | | |||| | ||| | || | |||| || | ||||||| |||||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||| ||| |||||| | ||
gtatgcacgttgaagtcttaatatataatgcagatatttggccttgtttgttctgttgcaatgcttattctaatgaacttgaaaattttgccaaatttcagGGTGCAAACATTCTTGTTGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTTGCAAAGTTG
upper sequence: GLYMA10G39670.1 (Glycine max), 3'ss of exon 5
lower sequence: AC197029.3_FGT003 (Zea mays), 3'ss of exon 5
gtattgtgcttttatttttactttttta----agattttctgccttggtatttgtctc-----tttatcatgttgatcaatgtgttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
|||| | | ||| | | | |||| || || ||| | || | | || | ||| | | | || | | ||||||| |||||||| || ||||| ||||||||||| ||||| ||||| ||||| ||||| ||| |||| | | ||
gtatgaacactgaagccttaacatataatggcagatctttggctttgcttgttctgttgaatgcttctaatgaaccttgaaattttccaaatttcagGGTGCAAACATTCTTGTAGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: GLYMA10G39670.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattgtgcttttatttttacttttttaagattttctgc-cttggtatttgtctctttatcatgttgatcaatgtgttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
|| ||| ||| || || | | |||| ||| || | | | | ||| | | ||||| || || ||| | || ||||||||||| ||||| | |||||| || |||||||| |||||||||||||| || ||
-----------gtactttcctctttccaacatgtgatatgcttgtggtttctcaaaattccgctataactcttgtcatattct-cctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA
upper sequence: GLYMA10G39670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
------------------------gtattgtgcttttattt--ttacttttttaagattttctgccttggtatttgtctctttatcatgttgatcaatgtgt-tgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
||||| | | | | |||||| | || | ||| | || || || | || | |||| ||| || |||| || || || || |||||||| || || ||||||||||| || |||||||||||||| |||||||||||||| |||
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTGMapped 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|192299835|gb|FG990072.1|FG990072EST: TGGGCCTTGAATATCTTCACAGTAACGGGATTATTCACAGGGATATTAAG GGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTT
genomic: TGGGCCTTGAATATCTTCACAGTAACGGGATTATTCACAGGGATATTAAGgtattgtgct ... ctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgccttggtatttgtctctttatcatgttgatcaatgtgttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
tgttgat putative branch site (score: 4)
tttatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtgcttttatttttacttttttaagattttctgccttggtatttgtctctttatcatgttgatcaatgtgttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA