Sequence
atgc intronic sequence ATGC exonic sequence...atatgtcaacatgtggaaccataatactaatcctatacatagtattgaaagaataattacattatatattgatccattcgggggcatgatatgatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
Basic information
species | Glycine max |
transcript | GLYMA17G36250.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G36250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10970.t01 (Vitis vinifera), 3'ss of exon 1
atatgtcaacatgtggaacc-ataatactaatcctatacatagtat-tgaaagaataattacattatatattgatccattcgggggcatgatat-gatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
||| || | || || | || | || ||| | | | | ||| | | | ||| | | | |||| || ||||| |||||||| ||||||||| |||||||||| || |||||||| | |||||||||||||| ||| |||| || |||||| | |||||||| ||
ataaaagaatgcaagtttcctgtattggaaaagcgttaaatacaagataagataatggatttaggtcacattaacca--caaacaatacaatattgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGTGGTATTGTGACTGCTATGCTGACTGCTCCGGATG-
upper sequence: GLYMA17G36250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g11010.t01 (Vitis vinifera), 3'ss of exon 1
atatgtcaacatgtggaaccataata--ctaatcctatacatagtattg---aaagaataattacattatatattgat-ccattcgggggcatgatat-gatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
|| ||| | | ||||| || |||| || || || || | || | | | | | | | | || | || || ||||| |||||||| ||||||||| |||| ||||| || |||||||| | ||||||||||||||||||||||| || |||||| |||||||||| ||
------cagaatgcgacctcctaatagtctctatttatatatgttactgctcaacacaagataatggattgaagtaacactaaccacaaacaatacattgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCTGACTACTTCGACGTGATTGCTGGAACAAGCACAGGAGGTCTTGTGACTGCTATGCTAACTGCTCCGGATG-
upper sequence: GLYMA17G36250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10980.t01 (Vitis vinifera), 3'ss of exon 1
atatgtcaacatgtggaaccataata----ctaatcctatacat-agtattgaaagaataattacattatatattgat-ccattcgggggcatgatat-gatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
| ||| | | ||||| ||| | |||| | | | | || | || | | || | | | | | | || | || || |||| |||||||| ||||||||| |||||||||| || |||||||| | ||||||||||||||||||||||| || |||||| |||||||||| ||
------aagaatgcgacctcttaatagtctctatttatatatgtcactgctcaacacaagataatgtattaaagtaacactaaccacaaacaatacattgaatcagGCGGTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGAGGTCTTGTCACTGCTATGCTAACTGCTCCGGATG-
upper sequence: GLYMA17G36250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10940.t01 (Vitis vinifera), 3'ss of exon 1
------atatgtcaaca-tgtggaaccata-atactaatcctatacatagtattgaaagaataattacattatatattgatccattcgggggcatgatat-gatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
| | ||||| | | || || || || | || ||| | || | ||| || | | | | | | || | || ||||| |||||||| ||||||||| |||||||||| || |||||||| | |||||||||||||| |||||||| | |||||| |||||||||| ||
aatgcgacctcccaacaatctcgatttgtatatgttactgctcaacacaagat-----aatggattgaggta-acactaacca--caaacaatacaatgttgaatcagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGACGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGGCTGCTATGCTAACTGCTCCGGATG-
upper sequence: GLYMA17G36250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10880.t01 (Vitis vinifera), 3'ss of exon 1
atatgtcaacatgtggaaccataatactaatcctatacatagtattgaaagaataattacattatatattgatc-cattcgggggcatgat--atgatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
|| | || || || | | | | | | | ||| || ||| ||| | | | | | | | || | || | || ||||| |||||||| ||||||||| |||||||||| || || ||||| | |||||||||||||| |||||||| || || ||| |||||||||| |
-aatcctcaaatatgttactgtggtccaagtgtcaaatataagat-aaaataatggatttaggtaacactaaccacaaacaatacaatattgaatatatcagGAGCTGGATGGTGATGATGCAAGGATTGCAGACTACTTCGATGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGACTGCCATGCTAACTGCTCCGAATG-
upper sequence: GLYMA17G36250.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10920.t01 (Vitis vinifera), 3'ss of exon 2
--atatgtcaacatgtggaaccataatactaatcctatacatagtattgaaagaataattacattatatattgatc-cattcgggggcatgat--atgatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
|| | || | || | | | | | | | ||| || ||| ||| | | | | | | | || | || | || ||||| |||||||| ||||| ||| |||||||||| || || ||||| | |||||||||||||| |||||||| || || ||| |||||||||| |
taatccctggctattt---actgtggtccaagtgtcaaatataagat-aaaataatggatttaggtaacactaaccacaaacaatacaatattgaatatatcagGAGCTGGATGGTGATGATGCGAGGATTGCAGACTACTTCGATGTGATTGCTGGAACAAGCACAGGTGGTCTTGTGACTGCCATGCTAACTGCTCCGAATG-Mapped 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|192322106|gb|FK012210.1|FK012210EST: GGGCATCATCCCCGCTACCATTATTGATTTCCTTGAATCTCGGCTTCAGG AATTGGATGGTCCGGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAG
genomic: GGGCATCATCCCCGCTACCATTATTGATTTCCTTGAATCTCAGCTTCAGGtatatcatct ... atgatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaagaataattacattatatattgatccattcgggggcatgatatgatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
tattgat putative branch site (score: 3)
aataattacattatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatgtcaacatgtggaaccataatactaatcctatacatagtattgaaagaataattacattatatattgatccattcgggggcatgatatgatgcaggAATTGGATGGTCCAGATGCAAGGCTTGCAGACTATTTTGACGTGATATCAGGAACAAGCACAGGAGGTCTTGTAACCGCTATGATAACTGCTCCAGACAA
- - - - acatgtg
- - - - - - - - - - - - - - - - - - - - - - - - aagaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgat