Sequence
atgc intronic sequence ATGC exonic sequencegtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttttctgaagaaatatgatgaaagcttaagttctgacgttattgtgttttaaattttttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG
Basic information
species | Glycine max |
transcript | GLYMA13G42070.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttt-tctgaagaaatatgatga-aagcttaagttctgacgttattgtgtttta-aattttttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG
|| | || || || ||| | | | || | | ||| || | | | | |||||| | | | | ||| | | | |||| || || | |||| || || || | |||||| ||||||||| | |||||||||| ||| || |||||||||||||| ||||| |||||||||||||| ||| | || ||||
------------------------------------------ttacttga--accgtttcctcagctgcacatttatttgtgtcttaaatatcaagtcaacaagcttg---tttagcagtcttgcggataacaattcttcttttcagGTGCCATGTCTTACGGACAACTATGCTTATATCTTACATGATGAGGATACCGGTACAGTTGGTGTGGTTGACCCTTCTGAAGCTGTACCTGTTATGGATG
upper sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G43430.2 (Arabidopsis thaliana), 3'ss of exon 1
gtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttttctgaagaaatatgatgaaagcttaagttctgacgttattgtgttttaaattttttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG
| | |||| || | ||| || || | || |||| | ||| || |||| | | | ||| | | | | | | | ||| |||| || ||| |||||||| |||||||||||||| || |||| ||||| || |||||||| || |||||||||||||| |||| ||| | ||||| |
---------------------------------gttagtatgcttttcatcttgaat----ctactggttgaaacaa---ctctgtaacaatctgctgaagat---attattaacgatctattttactgagatgtttc----agGTGCCCTGCAGTAAGGACAACTATGCTTATCTGTTGCACGATGAAGACACCGGAACAGTTGGAGTCGTTGATCCTTCTGAGGCTGCACCTGTTATAGAAG
upper sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G31350.1 (Arabidopsis thaliana), 3'ss of exon 2
----gtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttttctgaagaaatatgatgaaagcttaagttctgacgttattgtgttttaaattttttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG
||| || ||| | | | ||| | ||| ||| || | |||| |||| | | | || | ||| || | | | | || ||| | | || || || |||| |||||||| ||||| || ||||||||| | || ||||| | ||| || ||||||||||| || ||||| ||||||||||||| ||||| || |||
gtgcgtgctgttgggaatctcctaaaccattt----tctcacagtact------tactaatttggtctctag--------atttgtttgagcccatgtagtaggttatcatgtaatgaaaatgattcccaggtgtttattctttccagGTGCCTTGCCTTAAGGATAACTATGCTTATATCTTGCATGACGAGGATACTGGTACAGTTGGGGTGGTTGACCCTTCTGAAGCTGAACCTATTATCGATT
upper sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 4
gtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttttctgaagaaatatgatgaaagcttaagttctgacgttattgtgttttaaatttttt--ttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG
|| || | | | | | || ||| | || || || ||| |||| | | || ||| ||| || | | | | | | || ||||| | | ||||||| || ||||||||||| ||||| ||||| |||||||| || || || || |||||||| |||||||||||||||||||| || ||| | |||||||
--------------------------------cttaattgactcacttggtaac--ttaattgactcgc-ttggtaacagttct-------ttttgtg----cttcctttcacacataaatctttgtcaactttttccgtcttcagGTACCATGTCTGAAGGACAACTATGCATATCTTTTACATGACGTCGATACAGGCACAGTTGGAGTTGTTGATCCTTCTGAAGCCGTACCTGTTATAGATGMapped 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|6483209|gb|AW202389.1|AW202389EST: CTCAATTTTGCAGTGTTGCCAATATGTCTTCCTCATTGCAGATTGAATTG GTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACG
genomic: CTCAATTTTGCAGTGTTGCCAATATGTCTTCCTCATTGCAGATTGAATTGgtgagagcag ... tttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACG
EST:
gi|193481636|gb|FK446041.1|FK446041EST: TGTTGCCAATATGTCTTCCTCATTGCAGATTGAATTG GTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACG
genomic: TGTTGCCAATATGTCTTCCTCATTGCAGATTGAATTGgtgagagcag ... tttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACG
EST:
gi|10232754|gb|BE801642.1|BE801642EST: CTCAATTTTGCAGTGTTGCCAATATGTCTTCCTCATTGCAGATTGAATTG GTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACG
genomic: CTCAATTTTGCAGTGTTGCCAATATGTCTTCCTCATTGCAGATTGAATTGgtgagagcag ... tttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatgatgaaagcttaagttctgacgttattgtgttttaaattttttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG
ttctgac putative branch site (score: 2)
ttttttttgtt putative PPT
ttattgtgttttaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagagcaggtctcttatcagtcttttctgttttcatagtgctattggattacaattaggtcacccgtgctgataagttttctgaagaaatatgatgaaagcttaagttctgacgttattgtgttttaaattttttttgttagGTACCTTGCCTGAAGGACAATTATGCTTATCTGTTACATGATGTGGACACGGGTACAGTTGGTGTTGTTGATCCTTCTGAAGCTGTGCCTATCATAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG