Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgctttttggttcacttagctgcagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
Basic information
species | Glycine max |
transcript | GLYMA17G00570.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 8
gtatgtgctttttggttcacttagctgcagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
||| || || | | | |||| ||||| ||| ||| || || | || || | | |||||| | |||||| || ||||||||||| ||||||||||| |||| ||||||||||| ||||| || |||| || |||||| | ||| | || || |||||||||||
gtacgtaatt---gatgctctta----cagtaatagataaatagcatctgtttacttgatcaaaatatgttttcga------tattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATCTGCAATTATAGTATCTCGTCCTGAA
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 6
-gtatgtgctttttggtt--cacttagctg-cagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgt--gctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
| ||| | || | ||||| || | | | |||| | ||| ||| | | || ||| | | | | |||||| | |||||| || ||||||||||| ||||||||||| |||| ||||||||||| ||||| || |||| || |||||| ||| | || || |||||||||||
aggatgaggaagatgatgagtacttaattgatgctcttacagtaatagataaatgttatctgtttacttgatcaaaatatgttttcgatattttctccagTGAGAGCGCAAATGAATACACAGATGATGAGGATGCAAGCTGGAAAGTCCGGAGGGCTTCAGCAAAGTGCTTATATGCAATTATAGTATCTCGTCCTGAA
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 8
gtatgt-gctttttggttcacttagctgcagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
||| || || || | | || | | | || | | | | | || || | | |||| | || | ||| || |||||| ||||||||||| || ||||||||||| |||| ||||||||||| || || ||| |||| || ||| || | ||| | || || |||||||||||
gtacgtcactattatgctgacagcgattccatacagattaattagctcca----gtttgtgtaattaaaacttttaa-----cattttgttccagTGAGAGTGCAAATGAGTACACAGATGATGAGGATGCAAGCTGGAAAGTCCGTAGGGCATCAGCAAAGTGCCTATCTGCAATTATAGTGTCTCGTCCTGAA
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G053644_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------gtatgtgctttttggttcacttagctgcagta----tgggattaatgttttcatgatattcttcttgt-taatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
| || ||| | | | || | || | || || || ||| | | || |||| |||| | | | ||| || |||||| ||||||||||| || ||||||||||| |||| ||||||||||| || || ||| || | || ||| || | ||| | || || |||||||||||
gtatgttcccctatttttgcgacttatggtgatgtcccttgctgtctcggcaataaagtatcaccagactgcaggatttaggccgcccaggtccaattgtattgtaataaaaacttttaaactggtcagtttgtgtaattaaaactttttaacattttgttccagTGAGAGTGCAAATGAGTACACAGATGATGAGGATGCAAGCTGGAAAGTCCGTAGGGCATCATCAAAGTGCCTATCTGCAATTATAGTGTCTCGTCCTGAA
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgtgctttttggttcacttagctgcagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
|| || || || | | | || | | | || | | | | | | | | | || | | | ||| | ||| || ||||||||||| || |||||||||||||||| ||||||||||||| |||||||||| || |||||| |||||| ||| || ||||| ||| |||||
----gtaagttctgatttattca-ttggaacagtagcctagc-tccttacggtgcaccattatctcactgaaataagtct-ttctttctcacagCGAGAGTGCAAATGAGTACACAGATGATGAAGATGCCAGCTGGAAAGTTAGGAGAGCAGCGGCCAAATGCCTAGCAGGATTAATCGTTTCGCGTTCTGAG
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 9
gtatgt-gctttttggttcacttag--ctgcagtatgggattaatgttttcatgatattcttcttgttaatcttccca-aatgtgctatttt----ttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
|||||| | | ||||| | || || ||| | | ||| ||| || | |||||| | | || | | ||| || ||| ||||| ||||||| |||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| |||||
gtatgttgttcactggtttatgtatatttgagctatcgtgtaaataatttatgcatgcttgaattgttactaatatcacagtactgtatcttgtatttgtagTGAGAGTGCAACTGAATATACAGATGATGAGGATGTCAGCTGGAAAGTTCGAAGAGCAGCAGCTAAATGCTTAGCAGCTTTGATTGTTTCTCGACCTGAA
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S337_6V6.1 (Physcomitrella patens), 3'ss of exon 7
gtatgtgctttttggttcacttagctgcagtatgggat----taatgttttcatgatattcttcttgtt--------aatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
||| | | | | |||| || | | || | |||||| | ||| ||| ||| | || || ||| || | ||||| || |||||| |||| |||| |||||||||||| | ||||||||||| || || || |||||||| |||||| | || | || ||| | ||||||
------ccttacttgcagaataagcttgagaactgcatctcttgatgtttcactcttatcattcatgtcttcgacgggagatttaactatctgcgtttctgtgcagGGAGAGTGCAGATGAGTATAGTGATGATGAAGATATGAGCTGGAAAGTACGAAGGGCTGCAGCTAAGTGCTTATCGGCTGTAATCTCTTCGAGACCTGAG
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ33911 (Selaginella moellendorffii), 3'ss of exon 7
gtatgtgctttttggttcacttagctgcagtatgggattaatgttttcatgatattcttct-tgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
| ||||| || | || | | | | | | ||||| | | ||| || || || | || || | || ||||||||||| |||||||| || |||||||| ||||| |||||| | | ||| | || || | || |||
--------------------------------------gtaggtttttattacgtttccccatcctgctgaagtattaagagctatgtct--cagGGAGAGCGCTGACGAGTACAGTGACGATGAAGATGTAAGCTGGAAGGTGCGGAGAGCTGCAGCAAAATGCCTTTCTGCAGTTATCTCATCGAGACCGGAG
upper sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ37421 (Selaginella moellendorffii), 3'ss of exon 7
gtatgtgctttttggttcacttagctgcagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
||| | ||| | || | | || || ||| | | | ||||| | | ||| || || || | || || | || ||||||||||| |||||||| || |||||||| ||||| |||||| | | ||| | || || | || |||
-----------------------------gtaggtttttattacgtt-----tccccatcctgctaaagtattaaga---gctatgtct--cagGGAGAGCGCTGACGAGTACAGTGACGATGAAGATGTAAGCTGGAAGGTGCGGAGAGCTGCAGCAAAATGCCTTTCTGCAGTTATCTCATCGAGACCGGAGMapped 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|207685158|gb|GD669050.1|GD669050EST: AACATGGAGGAGGATACTGATGACGAAGGTCTTGAAGAGGAGGAGGATGA TGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCG
genomic: AACATGGAGGAGGATACTGATGACGAAGGTCTTGAAGAGGAGGAGGATGAgtatgtgctt ... ttttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgttttcatgatattcttcttgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
tgttaat putative branch site (score: 3)
ctatttttt putative PPT
tatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgctttttggttcacttagctgcagtatgggattaatgttttcatgatattcttcttgttaatcttcccaaatgtgctattttttgcagTGACAGTGCAAATGAATATACAGATGATGAAGATGTCAGCTGGAAAGTTCGGAGAGCAGCAGCTAAATGCTTAGCAGCATTGATTGTTTCTCGTCCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT