Sequence
atgc intronic sequence ATGC exonic sequence...tcttcatgaagtaaataaattatgccaattcataattttcctgaattgaaattggttcaaattcttaatgtgccttggtgtgactaatggatatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTCTTCAATTGGTTGGTGGCCTTCTCCCTGGTTATGGTAGTGATTGGCCGCT
Basic information
species | Glycine max |
transcript | GLYMA10G03660.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 15
tcttcatgaagtaaataaatta--tgccaattcataattt-tcctgaattgaaattggttcaaattcttaatgtgccttggtgtgactaatggatatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTCTTCAATTGGTTGGTGGCCTTCTCCCTGGTTATGGTAGTGATTGGCCGCT
| ||| | || || || |||| | || | || | | || || ||| | ||| || |||||| | | |||||||| |||| ||||| |||||||||||| ||| |||||||||||||||||| |||||||||| || ||||| || ||||| ||||
---tgatgtattacccctttttcttgtcaatctgcaggttgtttctaactcttgctaattatgatatttatctaaataaactctgatatgatatcgcatacagATGCTTGTCAAGTCTCGTGCTCTTTTTATCAAGGAGTACAATAACAAGCTCTTCAATTGGTTGGTAACCTTCTCCCTAGTCATGGTGGTTATTGGGCGCT
upper sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G019361_T03 (Zea mays), 3'ss of exon 14
tcttcatgaagtaaataaattatgccaattcataattttcctgaattgaaattggttcaaattcttaatgtgccttggtgtga---ctaatg----gatatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTCTTCAATTGGTTGGTGGCCTTCTCCCTGGTTATGGTAGTGATTGGCCGCT
| | ||||| | | | || | ||| || ||| | ||| ||| | | ||| ||| | | | | | | | | | ||||| | | |||||||| |||| || || |||||||||||| ||| ||| ||||||||||||||| ||||||| |||| ||||| || || || ||||
--ctactcaagtatgtgctctgt-----ttggttgcttttactctttaaaacttgttgtgatttgcatggagccatggactaagctccagtttgatgctgtgtttagATGCTTGCCAAGTCTCGTGCTCTTTTCATCAAGGAGTACAATAACAAGCTTTTCAATTGGTTGGTGACCTTCTCTTTGGTCATGGTGGTCATCGGGCGCT
upper sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G321413_T01 (Zea mays), 3'ss of exon 8
tcttcatgaagtaaataaattat--gccaattcataattttcctgaattgaaattggttcaaattcttaatgtgccttggtgtgactaatggatatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTCTTCAATTGGTTGGTGGCCTTCTCCCTGGTTATGGTAGTGATTGGCCGCT
| | ||||| | | | | | || | || | ||| | | || | ||| | | | | | | | | ||||| | | |||||||| |||| || || |||||||||||| ||| ||| ||||||||||||||| ||||||| |||| ||||| || || || ||||
--ctactcaagtatgtgctctgtttggttgcttttactctttaaaacttgttgtggtttgcatggagccatggactaagctccagtttgatgctgtgtttagATGCTTGCCAAGTCTCGTGCTCTTTTCATCAAGGAGTACAATAACAAGCTTTTCAATTGGTTGGTGACCTTCTCTTTGGTCATGGTGGTCATCGGGCGCT
upper sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 14
tcttcatgaa-gtaaataaattatgccaattcataattttcctgaattgaaattggttcaaattcttaatgtgccttggtgtgactaatggatatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTCTTCAATTGGTTGGTGGCCTTCTCCCTGGTTATGGTAGTGATTGGCCGCT
| | || | | | ||| || | || || | ||||| | || | | | || | |||| || | | || ||||||||||| ||||||||| ||||| ||||| |||||||| || |||||||||||||||||| |||||||||||||||| | ||||| ||| | ||||| |
tgtccaaaagtgccattaatttttcattcatcttacatatcctgtctccttgttatgttccctcgattataactatgtttgtgcctg-tataaatctgcagATGATGCAGAAGTCTCGATCTCTATTTATTAAGGAGTATAACCACAGGCTCTTCAATTGGCTGGTGGCCTTCTCCCTCTTCATGGTGGTGGTGGGCCGGTMapped 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|208157770|gb|GD957775.1|GD957775EST: GACCTTCAAAAACAAATTACGAGTTACGCATGATGAAG ATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTC
genomic: GACCTTCAAAAACAAATTACGAGTTACGCATGATGAAGgtctgataca ... atatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTC
EST:
gi|208336149|gb|GE134248.1|GE134248EST: GACCTTCAAAAAACAAATTACGAGTTACGCATGATGAAG ATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTC
genomic: GACCTTC-AAAAACAAATTACGAGTTACGCATGATGAAGgtctgataca ... atatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaaattggttcaaattcttaatgtgccttggtgtgactaatggatatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTCTTCAATTGGTTGGTGGCCTTCTCCCTGGTTATGGTAGTGATTGGCCGCT
gactaat putative branch site (score: 2)
ttcaaattcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttcatgaagtaaataaattatgccaattcataattttcctgaattgaaattggttcaaattcttaatgtgccttggtgtgactaatggatatatgcagATGATGGGGAAGTCTCGGTCTCTGTTTATAAAGGAGTACAATCACAGGCTCTTCAATTGGTTGGTGGCCTTCTCCCTGGTTATGGTAGTGATTGGCCGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- ttcatga
- - - - - - aaataaa
- - - - - - - - - - tatgcca
- - - - - - - - - - - - - - - - - - - tcctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaatgg