Sequence
atgc intronic sequence ATGC exonic sequence...agatcttatccctttctttcccccctaacagtctaggcatttcactttactagaatattgtaggctgagggtttttcctactttgcaacttgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCCTGGAAAAGAGGAAGTTCAAATGTTCCATGAGGCTTACGATGTTGTACTT
Basic information
species | Glycine max |
transcript | GLYMA13G20980.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------------------agatcttatccctttctttcccccctaacag------tctaggcatttcacttta--ctagaata------ttgtaggctgagggtttttcctactttgcaacttgttat---gcagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCCTGGAAAAGAGGAAGTTCAAATGTTCCATGAGGCTTACGATGTTGTACTT
| | | ||| | |||| || || || ||||| | | | | || || | || || | ||| ||| | ||| || || ||||||||||| || ||||||||||| ||||||||||||| ||| | |||||||| || ||| | |||| ||||| || || |||
gtgaatatcttctttccttgtaagaaaccctctttacagccatggctctgagttgcttgcaccccaagcattccattacaaggaaaagtttcctcatgttgcacttcatcccaaagtaggagggttaccaatcaggtgtcttactctttttttgtgttgacacttgacagGCTGCAGATCCAGCTAGGGGTTAACATGCCTGCAAGGGCAGAGCAGAACCCTAAAGAAGAGGAAAGCAAATCGTTTCGGGAGGTGTACGACGTGGTCCTT
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 8
----------------------------agatcttatccctttctttcccccctaacagtctaggcatttcactttactagaatattgtaggctgagggtttttcctactttgca-acttgttatg-----cagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCCTGGAAAAGAGGAAGTTCAAATGTTCCATGAGGCTTACGATGTTGTACTT
| ||| | | | | || | || | | || | || | || | ||||| | | || ||||| ||| || || ||||||||||| || ||||||||||| ||||||||||||| ||| |||| ||| || ||||| ||||| |||||||| || ||
gtaactttctgtagttcaaatactttgagtagcttgtggacattgtgttgcgctggcgtgctgcttgtgtagtttcgaaggggtagaatttgcaggttctttttaaaaaaaaacgtgtttcttatgtttgtcagGCTTCAGATCCAGCTAGGAGTTAACATGCCTGCAAGGGCAGAGCAGACCCCTAAGGAAGATGAAAGCAAACCGTTCCGTGAGGTGTACGATGTGGTCCTC
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 8
------------agatcttatccctttctttcccccctaacagtctag--gcattt-cactttactagaatattgtaggctgagggtttttcctactttgcaacttgt-tatg-cagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCCTGGAAAAGAGGAAGTTCAAATGTTCCATGAGGCTTACGATGTTGTACTT
| || || | || | | | | | | ||||| | ||| | | | | |||| || | ||||| | || ||| || || ||||||||||| || ||||||||||| ||||||||||| || | |||| | | || || | |||| |||||||| || |||
gtaattgtttgtggctcagatactttgagtggctttgtggaaattgtgttgcattggcggggagctacagcagcttcttttattttatttttgtaatgcctttcttgtgtttgtcagGCTTCAGATCCAGCTAGGAGTTAACATGCCTGCAAGGGCAGAGCAAATCTCCAAGGAAGACGGAAGCAAATCATTTCGCGAGGTGTACGATGTCGTGCTT
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 7
---agatcttatccctttctttcccccctaacagtctaggcatttcactttactagaatattgtaggctgagggttttt-cctactttgcaacttgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCCTGGAAAAGAGGAAGTTCAAATGTTCCATGAGGCTTACGATGTTGTACTT
||| | || || | | | | |||| || || | | || | | | || | | |||| || | ||| ||||||| ||||||||||| |||||||| ||||| || |||||||| ||||| | || | | ||||||| | | | || || | |||||||||||
actagaaatattcatgttgtgtgagtagaaggtgagatggcaaaa-acattcttgttttctttcaatatctgaattctaattttctttttgacctcttaagCAGACTCCAAATCCAGCTTGGTGTGAATATGCCAGCAAGGGCAGAAAAGATTACAGGGATACAGGAAGTAGAGACACTTCACGAAACATACGATGTTGTT---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|5760794|gb|AI966157.1|AI966157EST: CGAGCTGCTGTGGATGAGGAGGTGGATCTACTTCTACCCGGTACAGCAAG ACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCC
genomic: CGAGCTGCTGGGGATGAGGAGGTGGATCTACTTCTACCCGGTACAGCAAGgtatggtttc ... tgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCC
EST:
gi|193441463|gb|FK405062.1|FK405062EST: TGAGGAGGTGGATCTACTTCTACCCGGTACAGCAAG ACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCC
genomic: TGAGGAGGTGGATCTACTTCTACCCGGTACAGCAAGgtatggtttc ... tgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttactagaatattgtaggctgagggtttttcctactttgcaacttgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCCTGGAAAAGAGGAAGTTCAAATGTTCCATGAGGCTTACGATGTTGTACTT
tagaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatcttatccctttctttcccccctaacagtctaggcatttcactttactagaatattgtaggctgagggtttttcctactttgcaacttgttatgcagACTACAAATCCAGCTAGGTGTGAACATGCCTGCTAGGGCAGAGCAGATTCCTGGAAAAGAGGAAGTTCAAATGTTCCATGAGGCTTACGATGTTGTACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - -ccctttc
- - - - - - - - -ttccccc
- - - - - - - - - - - - - - - - - - gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggctga