Sequence
atgc intronic sequence ATGC exonic sequencegtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
Basic information
species | Glycine max |
transcript | GLYMA17G08660.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G08020.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaa-atttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
| | | ||| ||| || || | || ||| | | | |||| | | |||||| ||| | || |||||| | ||| ||||| ||||| | ||||||||||| ||||| || || |||||||||| ||||| || ||||| || || |||||||||||||||
-----------------------------------------------------------------------gtacttcaaaacacttttaacatattaa--gatatggaaaaaagaaaagttgatttatgagtctcgtatatatatt---gcagCCTGTATTCTTCAGCACTAGAGCTTACATAAGCTTCATCAAGCCAGACCAAACAATGTGGTACCGTGCTTGCAAGACCTGTAACAAGAAAGTTACTGAAG
upper sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0047g00870.t01 (Vitis vinifera), 3'ss of exon 4
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
| || || | ||| | | | | || | || | ||| | || ||| || || | | ||| ||||| | | ||| | || || |||| ||||||| || | |||| | | ||||||||||| |||||||| || |||||||||| | || |||||||||||||| |||||||| || ||
------------------------------gtaataattactgtcattaaa----ataacctaacatgatca--aactggtcttagccaaagttttaa----gttaaaatcattttaagttttgataatgtgggcttgt----ctctgtatagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0065g00990.t01 (Vitis vinifera), 3'ss of exon 1
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
| | | || | || || | | || | | | | || | | | || || || | || ||| ||||| | ||| ||| | || | ||||| ||||| | ||||| || | |||| | | ||||||||||| ||||||||||| |||||||||| || || |||||||||||||| |||||||| || ||
------------------------gtaataattactgtcattagaataac-ctaacatgatcaacctggtc-ttagccaaagttttgag----ttaaaagcatattc---agttttga---taa--tgtgggcttgt------ctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0587g00010.t01 (Vitis vinifera), 3'ss of exon 4
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
| | | || | || || | | || | | | | || | | | || || || | || ||| ||||| | ||| ||| | || | ||||| ||||| | ||||| || | |||| | | ||||||||||| ||||||||||| |||||||||| || || |||||||||||||| |||||||| || |
------------------------gtaataattactgtcattaaaataac-ctaacatgatcaacctggtc-ttagccaaagttttgag----ttaaaagcatattc---agttttga---taa--tgtgggcttgt------ctttgtacagCCTTCCTTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGGTG
upper sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g07440.t01 (Vitis vinifera), 3'ss of exon 9
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
| || || | ||| | | || | || | || | ||| | || ||| || || | | | ||||| | | ||| | || || ||||| | ||||| || | || | | | ||||||||||| ||||||||||| |||||||||| || || |||||||||||||| |||||||| || ||
------------------------------gtaataattactgtcattaaa----ataacttaacatgacca--aactggtcttagccaaagtttt----gagttaaaaccatattcagttttgataatgtgggcttgt----ctctgtacagCCTTCCTTTTTTAGCATCAGGGCATACATAAGCTTCATCAAGCCTGATCAAACAATGTGGTACCGGGCTTGTAAGACATGCAACAAGAAAGTCACAGATG
upper sequence: GLYMA17G08660.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv03s0088g00230.t01 (Vitis vinifera), 3'ss of exon 5
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
| || || | ||| | | | | || | || | ||| | || ||| || || | ||| ||||| | | ||| | || || ||||| ||||||| || | |||| | | ||||||||||| |||||||| || |||||||||| | || |||||||||||||| |||||||| || ||
------------------------------gtaataattactgtcattaaa----ataacctaacatgatca--aactggtcttagccaaagttttaa----gttaaaaccattttaagttttgataatgtgggcttgt----ctctgtacagCCTTCATTTTTTAGCATCAGAGCATACATAAGCTTCATCAAGCCTGAGCAAACAATGTGGTACCAGGCTTGTAAGACATGCAACAAGAAAGTCACAGATGMapped 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|31310108|gb|CD395311.1|CD395311EST: CCCATCATTGGGGGATGTCAAG CCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAG
genomic: CCCATCATTGGGGGATGGCAAGgtatttggtt ... ctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
gtttaac putative branch site (score: 3)
ttgcttt putative PPT
tttcatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttggttgcaaattttcctgaatgttgggcattgctaatacgattccatctgcttgtttgatataaacattcattggaactcttagaaatttcaatggattttcattagtttctagtttaacttgtagtctcttatgttgctttgggcagCCCGCATTTTTCAGTCTTAGAGGACATATAAGCTTCATAAAGCCTGATCAGGCAATGTGGTATCGTGCCTGTAAGACATGCAATAAGAAAGTTACTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA