Sequence
atgc intronic sequence ATGC exonic sequence...caagagttgcatggattgaatgcctgactaactaactgatccaattgctatattctgtgaatattgatatcagcaattaatctaacatatttttctacagTTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTCGGGAGTG
Basic information
species | Glycine max |
transcript | GLYMA10G28310.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G28310.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G05870.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------caagagttgcatggattgaatgcctgactaactaactgatccaattgctatattctgtgaatattgatatcagcaattaatctaacatatt-tttctacagTTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTCGGGAGTG
| | ||| | | || | || | | | ||| | | | | || | | || | | | || | | | ||| |||||||||| | ||||| ||||| |||||| | |||||||| |||||||||||||||| ||||| ||||| |||||||| |||||| | | || ||
gtaaagttctcttctttcatgtcttcgcttttatatatgttgcttagaacacccactatttctcttgcttacggaaacattg-ctaaacatttacttatggtaataactcaaa-acaaaactgcatgcct-tagaccttatctgttttggtgttttggtgtttgggcagTTTGGGGAGCCTGCAACCACGCGTTTCATCTTCACTGTATATTGAAATGGGTGAATTCGCAGACGAGCCAAGCTCATTGCCCAATGTGCAGAAGAGAATG
upper sequence: GLYMA10G28310.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g03770.t01 (Vitis vinifera), 3'ss of exon 2
caagagttgcatggattgaatgcctgactaactaactgatccaattgctatattctgtgaatattgatatcagcaattaatctaaca-------tatttttctacagTTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTCGGGAGTG
|| || || || || ||| || | | || | | | ||| || | ||| | |||| | | || | || |||||||||||| ||||| || ||||||||| | || || ||| |||||||||||||||| ||||| | |||||||||||||||||||||||| |||| ||
------ttatatatat-aaaaaaaagattaaagaaacttttaagttttttttaggaattggtatcaatccaactaatgattctattaaccattgttttgtcctgcagTTTGGGGTGCTTGCAACCATGCATTTCATCTCCATTGCATCTTGAAATGGGTGAATTCGCAGACTCCTCAAGCGCATTGCCCCATGTGCCGTAGGGAATG
upper sequence: GLYMA10G28310.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g00290.t01 (Vitis vinifera), 3'ss of exon 5
caagagttgcatggattgaatgcctgactaactaactgatccaattgctatattctgtgaatattgatatcagcaattaatctaaca-------tatttttctacagTTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTCGGGAGTG
|| || || || || ||| || | | || | | | | ||| || | ||| | |||| | | || | || |||||||||||| ||||| || ||||| ||| | || || ||| |||||||||||||||| ||||| | |||||||||||||||||||||||| |||| ||
------ttatatatat-aaaaaaaagattaaagaaacttttaagtttttttttggaattggtatcaatccaactaatgattctattaaccattgttttgtcctgcagTTTGGGGTGCTTGCAACCATGCATTCCATCTCCATTGCATCTTGAAATGGGTGAATTCGCAGACTCCTCAAGCGCATTGCCCCATGTGCCGTAGGGAATGMapped 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|254317371|gb|GR826316.1|GR826316EST: TGATGGATGTTGTCCTGACTGTAAACTTCCTGGAGATGACTGCCCATTGA TTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGG
genomic: TGATGGATGTTGTCCTGACTGTAAACTTCCTGGAGATGACTGCCCATTGAgtaagctact ... ttttctacagTTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGG
EST:
gi|193360358|gb|FK325128.1|FK325128EST: TGATGGATGTTGTCCTGACTGCAAACTTCCTGGAGATGACTGCCCACTGA TTTGGGGTGTATGCAATCACGCATTTCATCTGCACTGTATCCTGAAATGGG
genomic: TGATGGATGTTGTCCTGACTGTAAACTTCCTGGAGATGACTGCCCATTGAgtaagctact ... ttttctacagTTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctatattctgtgaatattgatatcagcaattaatctaacatatttttctacagTTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTCGGGAGTG
atctaac putative branch site (score: 2)
tatttttct CT-rich tract
aattaatctaacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caagagttgcatggattgaatgcctgactaactaactgatccaattgctatattctgtgaatattgatatcagcaattaatctaacatatttttctacagTTTGGGGTGTATGCAATCACGCATTTCATTTGCACTGTATCCTGAAATGGGTGAATTCTCAGACATCACAAGCGCATTGCCCCATGTGCCGTCGGGAGTG
- - - - gcatgga
- - - - - - - - -gaatgcc
- - - - - - - - - - - - - - - - - -ctgatcc
- - - - - - - - - - - - - - - - - - - - - - -tgctata
- - - - - - - - - - - - - - - - - - - - - - - - - - ttctgtg