Sequence
atgc intronic sequence ATGC exonic sequence...ttttgaagtgtcttgtggaattggttacgcattaattatattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
Basic information
species | Glycine max |
transcript | GLYMA05G36850.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G64440.1 (Arabidopsis thaliana), 3'ss of exon 3
ttttgaagtgtcttgtggaattggttacgcattaattatatt--ttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttca----gCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
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-gtaaaatccccttttggtctgtattgcagatttttggtattccttatgtatgtgagtatgtgacagtgaaacatgatttaactttctctcattgatctcaatcagCTTGTATTTTCTTCGTCCGCTACTGTGTATGGCTGGCCAAAGGAGGTTCCTTGTACAGAAGAGTCTCCCCTGTCTGGAATGAGTCCTTATGGACGGACAA
upper sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 3
ttttgaagtgtcttgtggaattggt---tacgcattaattatattttcttgatgctgcaatctgattatttaac-tgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
||| |||| | ||| || || | | | | | |||| | || | ||||| || || || || || ||||||||||| ||||| ||||||||||| ||||||| ||||| || || || ||||| || ||||| || | || || ||||||||||||||||| |
----------gtatgtataatttgccactacacaacaagttcgaatccatttttactttgcttgatcaattctcatgattagctactt-ttactctgtttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA
upper sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G23920.1 (Arabidopsis thaliana), 3'ss of exon 3
------------ttttgaagtgtcttgtggaattggttacgcattaattatattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
|| || | ||||| | ||| ||| |||| | | | | |||| | | || ||| || | || || || |||||||| || ||||| ||||| ||||| ||||||||||| |||||||| || || || || |||| || | || || || ||||||||||| || || |
gtaatttttttccttcctctctctttttctaattgccaccacatgcattccctttttgagtttgtcttgtttgatctcattattggcttt-tactactctgt---tttccagCTTGTATTTTCATCATCAGCTACTGTCTATGGCTGGCCTAAGGAGGTTCCTTGCACTGAGGAGTCACCAATTTCTGCCACTAACCCATATGGCCGTACAA
upper sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 3
-ttttgaagtgtcttgtggaattggttacgcatta-atta-tattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
|| | | | | | | ||| | | | |||| | ||| || || ||| || | ||||| || | |||| | |||||||||||| || ||||| ||||| ||||| ||||| |||||||||||||| |||||||| ||||||||||| | | |||||||| |||||||||||||| |
tcctttattttttgtttttaccacgtttcttgtgatattactgtttatgtgcaactctgttctaatgtctccactgacttctaaattctc---aacatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCACTATGTGCAACAAATCCATATGGACGAACTA
upper sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
---ttttgaagtgtcttgtggaattggttacgcattaattatattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
| | | || | | || | | | | | ||| || || || || || |||||||| |||||| ||| |||||||||||| || ||||| ||||| ||||| ||||| |||||||||||||| |||||||| ||||||||||| | | || |||| ||||||||||||||||
agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctc--aat-atttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA
upper sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------ttttg-aagtgtcttgtggaattggttacgcattaattatattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
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gtgagaatatttcccaccacaggggtagctcaagtggatagacactcaatgttactactgctcagttctcgtgaatgtcttaagatagtggtta-gtgagaagcatcctaccattaaaattcg---tatctcttgaaattttaatatgagtggaccattggatgcagCTTGTGTTCTCATCTTCAGCAACAGTGTACGGACAACCGGAGTGCGTACCTTGTACAGAGGACTATCCACTCCATGTCATGAATCCTTACGGCCGCACCAMapped 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|192298481|gb|FG989187.1|FG989187EST: TAGGGACAATCGTTCTATTTGAAGTCATGGCTGCCCACGGATGCAAGAAG CTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCA
genomic: TAGGGACAATCGTTCTATTTGAAGTCATGGCTGCCCACGGATGCAAGAAGgtatattcat ... atgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCA
EST:
gi|17022675|gb|BM093709.1|BM093709EST: TAGGGACAATCGTTCTATTTGAAGTCATGGCTGCCCACGGATGCAAGAAG CTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCA
genomic: TAGGGACAATCGTTCTATTTGAAGTCATGGCTGCCCACGGATGCAAGAAGgtatattcat ... atgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
aactgat putative branch site (score: 3)
attatttaactgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttgaagtgtcttgtggaattggttacgcattaattatattttcttgatgctgcaatctgattatttaactgattttatatttctttgaatgatttcagCTTGTGTTCTCATCTTCAGCAACTGTATATGGCTGGCCAAAGGAGGTCCCATGTACCGAAGAGTTCCCTTTGTCAGCAACAAACCCATATGGACGAACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- -tgaagtg
- - - - - tcttgtg
- - - - - - - - - - - - - - - - - - - - - - -ttgatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcaatc