Sequence
atgc intronic sequence ATGC exonic sequence...catcagataaatgctacatgatgttagcaaacaacaatatggatgttattctttgggttgtcgtagtcttcataaagctaattgttgtttgattttgtagAGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCCATCGTTCATGTCTTGATCATTGGCGCTCAGTAAAG
Basic information
species | Glycine max |
transcript | GLYMA05G08220.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G08220.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g04730.t01 (Vitis vinifera), 3'ss of exon 3
catcagataaatgctac-atgatgttagcaaacaacaatatggatgttattctttgggttgtcgtagtcttcataaagctaa--ttgttgtttgattttgtagAGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCCATCGTTCATGTCTTGATCATTGGCGCTCAGTAAAG
|| | | | | | | || | | ||| | | ||| | ||| || |||| | | | | || ||||| ||| ||||| |||| ||||||||||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||||||||| ||||| |||
gatgcctttacttttgttgttcttttttctttcctaaatcttgttgtaa--cttgggcttgttcttttttctttggtctcaagattgtt-tttcattttatagATGATGAATTGATATCTCCATGCATGTGCAAAGGCACCCAACAGTTTGTTCATCGTTCATGCCTTGATCATTGGCGTTCAGTGAAG
upper sequence: GLYMA05G08220.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26224 (Selaginella moellendorffii), 3'ss of exon 1
catcagataaatgctacatga-tgttagcaaacaacaatatggatgttattctttgggttgtcgtagtcttcataaagctaattgttgtttgattttgtagAGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCCATCGTTCATGTCTTGATCATTGGCGCTCAGTAAAG
| | | || || | | | || | | || | || | ||||| | | | | || || ||||||||||| ||||| || |||||||| ||||| |||||||| |||||||| ||||| || ||||| |||||||| || |||
-----------------gtaagtctttgctagaatcgatctt--tcttccgtgctaagtaagaaaattcttctttggttttttacccttgatgcgttccagGCGATGAATTGATCTCTCCTTGTATGTGCAAGGGGACTCAACAGTTCGTCCATCGATCATGCCTCGATCACTGGCGCTCGGTCAAG
upper sequence: GLYMA05G08220.2 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14522 (Selaginella moellendorffii), 3'ss of exon 1
catcagataaatgctacatga-tgttagcaaacaacaatatggatgttattctttgggttgtcgtagtcttcataaagctaattgttgtttgattttgtagAGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCCATCGTTCATGTCTTGATCATTGGCGCTCAGTAAAG
| | | || || | | | || | | || | || | ||||| | | | | || || ||||||||||| ||||| || |||||||| ||||| |||||||| |||||||| ||||| || ||||| |||||||| || |||
-----------------gtaagtctttgctagaatcgatctt--tcttccgtgctaagtaagaaaattcttctttggttttttccccttggtgcgttccagGCGATGAATTGATCTCTCCTTGTATGTGCAAGGGGACTCAACAGTTCGTCCATCGATCATGCCTCGATCACTGGCGCTCGGTCAAGMapped 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|21600809|gb|BQ611140.1|BQ611140EST: GTCGAATTTGCCTCGAAAGCGATTCCGACCCAG AGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCC
genomic: GTCGAATTTGCCTCGAAAGCGATTCCGACCCAGgtgaaaattc ... gattttgtagAGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCC
EST:
gi|151412097|gb|EV281909.1|EV281909EST: TGGATTACTCCCCTGTTGTCGAATTTGCCTCGAAAGCGATTCCGACCCAG AGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCC
genomic: TGGATTACTCCCCTGTTGTCGAATTTGCCTCGAAAGCGATTCCGACCCAGgtgaaaattc ... gattttgtagAGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattctttgggttgtcgtagtcttcataaagctaattgttgtttgattttgtagAGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCCATCGTTCATGTCTTGATCATTGGCGCTCAGTAAAG
tttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catcagataaatgctacatgatgttagcaaacaacaatatggatgttattctttgggttgtcgtagtcttcataaagctaattgttgtttgattttgtagAGGATGAATTGATATCTCCGTGCATGTGCAAAGGGACCCAACAGTTTGTCCATCGTTCATGTCTTGATCATTGGCGCTCAGTAAAG
- - - - - -tgctaca
- - - - - - - - - tgatgtt
- - - - - - - - - - - - - gcaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - gggttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt