Sequence
atgc intronic sequence ATGC exonic sequencegtccgaaaattgttattggttaatgatttatattttgatctgtcaatttctaatcttcatttaacctgtgtgtaaactacttgtttagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG
Basic information
species | Glycine max |
transcript | GLYMA18G51310.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 6
gtccgaaaattgttattggttaatgatttatattttgatctgtca-atttctaatcttcatttaacctgtgtg--taaactacttgtttagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG
| ||| || | || |||| ||| | | | | | |||| || || ||| | | || | |||| ||| ||||| ||||| | ||||| ||||||||||| ||||||||||| || ||||| || ||||| || || |||||||||||| |||||||||| || ||||||
----gtaaaggcgcatagctt--ctatttgtataatatttttttatgtttccaagtttagtttcagttttgagatcgaacttgctgtgtagGTTGGCCCAAGGTTCTGTTTGAACCCAATCAAAATATTTGGCGGTAGTTTCGGTGGCCCTACATTGTACGAGAATCCATTCTATGTGTCTCCCAATCAG
upper sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G168176_T02 (Zea mays), 3'ss of exon 6
gtccgaaaattgttattggttaatg-atttatattttg-atctgtcaatttctaatcttcatt-taacctgtgtgtaaactact-tgtttagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG
||||| | | | | || ||| ||| | || | | ||| || ||| |||| | | | || | | ||||| ||||| | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |
-----gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataataatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATG----------------------------------
upper sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G160458_T01 (Zea mays), 3'ss of exon 6
gtccgaaaattgttattgg-ttaatgatttatattttgatctgtcaatttctaatcttcatt-taacctgtgtgtaaactacttgtt-tagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG
|| || | | || | || ||| | | | || | | | | || ||| |||| | | | || || ||||| ||||| | ||||| ||||| ||||| |||||||||||||| |||||||| || || || | || ||||| ||| ||| | || || ||||||
-----gtaactgcactgagcttctttatggatactcaggtgcttcccagttttgtataaataataaattgtgc-tggattgctctttgtagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG
upper sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
gtccgaaaattgttattggttaatg-atttatattttg-atctgtcaatttctaatcttcatt-taacctgtgtgtaaactact-tgtttagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG
||||| | | | | || ||| ||| | || | | ||| || ||| |||| | | | || | | ||||| ||||| | ||||| ||||| ||||| |||||||||||||| |||||||| || || || | || ||||| ||| ||| | || || ||||||
-----gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataataatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG
upper sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 6
gtccgaaaattgttattggttaatgatt-tatattttgatctgtcaatttc--taatcttcatttaacctgtgtgtaaactacttgtt--tagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG
|| |||| || | || ||||| || | || || | | |||| | |||| || | |||| ||||| ||||| || || |||| || ||||| || || || |||||||||||||| |||||||||||||| ||||| ||||||||| | || | ||||||||| ||
gtttgaaa--tgattcacctttctgattatagaacttatctagttgttgtaaataattctagcttaatcttgg----aactggttgttgatagGTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAGMapped 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|151404906|gb|EV274720.1|EV274720EST: AAGCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATCGAG GTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
genomic: AAGCGGACAAATTACCTAGAGGTGGCCTTGATAAAATGACATTGATCGAGgtccgaaaat ... acttgtttagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatctgtcaatttctaatcttcatttaacctgtgtgtaaactacttgtttagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG
cttgttt CT-rich tract
taatcttcatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccgaaaattgttattggttaatgatttatattttgatctgtcaatttctaatcttcatttaacctgtgtgtaaactacttgtttagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG