Sequence
atgc intronic sequence ATGC exonic sequenceagtaagtttttgctgtttattccttttagatatctatttgatttggtgcatgcgatgtttgtgttctttctgaaagtcatgtcctagtttttttgtgtctgatggtcaatatgatatatcgtgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCCGATCAGATAAGGGAATTGAGGGAA
Basic information
species | Glycine max |
transcript | GLYMA17G37220.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G37220.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------agtaagttt----ttgctgtttattccttttagatatctatttgatttggtgcatgcgatgtttgtgttctttctgaaagtcatgtcctagtttttttgtgtctgatggtcaa-tatgatatatcgtgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCCGATCAGATAAGGGAATTGAGGGAA-
||| || ||| || ||| ||| ||| | || ||| |||| ||| | ||| ||| | | |||| | ||||| | || ||| || | | | || ||| | || | ||||||||||||| ||||| || ||| |||| || |||||||||||| |||| ||||| ||||| ||||| ||||| ||||| || | ||| | ||||||
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatg-att--attttcaacatttta-gttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT
upper sequence: GLYMA17G37220.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 3
agtaagtttttgctgtttattccttttagatatctatttgatttggtgcatgcgatgtttgtgttctttctgaaagtcatgtcc-tagtttttttgtgtctgatggtcaatatgatatatcgtgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCCGATCAGATAAGGGAATTGAGGGAA-
|||| ||| || || || | ||| || |||| || || | ||| | ||||| || | || | | | | || ||| | |||||||||| ||||| ||||| ||||| || ||||| ||||||||||| || ||||| |||||||| || || || || || | ||| | | ||
-------------------------ttaggatcttatatgttt------gtgagtcgttggtaaaatttccaaatatcttctccgctgatttttcgt-tttgtgcatttgtgcgcttgatt-cgtgcggttagGTTGATCCCGTAGTGTACAACATGCTTCACGAGGACCCTGGTAATATTAGCTACTCAGCTGTTGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGT
upper sequence: GLYMA17G37220.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S91_182V6.1 (Physcomitrella patens), 3'ss of exon 3
agtaagtttttgctgtttattccttttagatatctatttgatttggtgcatgcgatgtttgtgttctttctgaaagtcatgtcctagtttttttgtgtctgatggtcaatatgatatatcgtgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCCGATCAGATAAGGGAATTGAGGGAA-
|| | |||||| || | | || | | ||| |||| | | || | | | | ||| | | ||| || | |||||| |||||||||| || || |||||||||||||| ||||| ||||| ||||| || ||||| || ||||| || | ||||| || | || | | ||
-------------------ttgttcatagatacctg---ggct--gtctaaacagtgtctgtgcttactttgccgattgtat----gcctttatataaaaaatgtgcatgtctgtgcgat-tgtgtt---agGTTGATCCCGTTGTGTACAATATGCTGCACGAGGACCCTGGAAATATTAGCTACTCAGCCGTTGGAGGACTCAGTGATCAAATCCGAGAGCTCCGTGAGTMapped 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|298188174|gb|HO034867.1|HO034867EST: GTCGTTCTTGATATGACGACGCTCACCATAATGCGGGCTCTTCCACGTGA AGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAG
genomic: GTCGTTCTTGATATGACGACGCTCACCATAATGCGGGCTCTTCCACGTGAagtaagtttt ... tgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAG
EST:
gi|16281445|gb|BI944491.1|BI944491EST: GTCGTTCTTGATATGACGACGCTCACCATAATGCGGGCTCTTCCACGTGA AGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAG
genomic: GTCGTTCTTGATATGACGACGCTCACCATAATGCGGGCTCTTCCACGTGAagtaagtttt ... tgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgtcctagtttttttgtgtctgatggtcaatatgatatatcgtgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCCGATCAGATAAGGGAATTGAGGGAA
gtctgat putative branch site (score: 4)
tcaatatgatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtaagtttttgctgtttattccttttagatatctatttgatttggtgcatgcgatgtttgtgttctttctgaaagtcatgtcctagtttttttgtgtctgatggtcaatatgatatatcgtgtgttgacaGGTTGATCCAGTAGTTTACAATATGCTGCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCCGATCAGATAAGGGAATTGAGGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG