Sequence
atgc intronic sequence ATGC exonic sequence...agttgtatacttcacagtctgttgttaagagccatatagccttctatatgcatgtctgggagcagggagttgttcatgcctttaatttatctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCTCCCATCTTACTACGTTGTAAACATATTTTCTGTGAAGATTGCGTATCAG
Basic information
species | Glycine max |
transcript | GLYMA18G45010.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 3'ss of exon 6
agttgtatacttcacagtctgttgttaagagccatatagccttctatatgc-----atgtctgggagcagggagttgttcatgcctttaatttatctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCTCCCATCTTACTACGTTGTAAACATATTTTCTGTGAAGATTGCGTATCAG
|| | ||| || || ||| ||| || | | | | ||| | | | | ||||| | || || ||| || ||||| | ||| ||||||||| | ||||| || |||||||| |||||||||| ||| || | || || |||||||||||||||||||| || || || || |
taacacgtattcgctagttggtacttggtagcaggatacccccttgaactctcactctatcttgtttaaagaacttgttttttgctggaac----ctggtg-cagGTAATTGCTGCTGGTGATATGTGTGCCATCTGCCAGGAAAAGATGCATGTTCCTGTCCTCCTCCGCTGTAAACATATTTTCTGTGAGGACTGTGTCTCTG
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G061980_T01 (Zea mays), 3'ss of exon 6
--agttgtatacttca--cagtc-tgttgttaagagccatatagccttctatatgcatgtctgggagcagggagttgttcatgcctttaatttatctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCTCCCATCTTACTACGTTGTAAACATATTTTCTGTGAAGATTGCGTATCAG
|| |||| | | || | | ||||| ||| | | | || || || | || | ||||||| | | | | || | | |||||| ||| ||||||||| | ||||| |||||||||||||||||||||| || | | || || ||||||||||||||||||||||| || || || |
agagccttataagttatccaatgattttgttgtgagtccttaggatttgaatttgaaaatcctgttatt---agttgtt--ttcttattgttgggcctaatgcagGTACTTGCTGCTGGTGATATGTGTGCCATTTGCCAGGAGAAGATGCATGTGCCTGTTCTCCTTCGCTGTAAACATATTTTCTGTGAAGACTGTGTTTCCG
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G141216_T02 (Zea mays), 3'ss of exon 6
agttgtatacttcacag--tctgttgttaagagcc-atatagccttct-atatgcatgtctgggagcagggagttgttcatgcctttaatttatctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCTCCCATCTTACTACGTTGTAAACATATTTTCTGTGAAGATTGCGTATCAG
|| | || |||| || | | | || | |||| | || | | | || || || | ||| | | |||| ||||| ||| ||||| || | ||||| || ||||| || |||||||||| ||||||| | | || || |||||||| |||||||||||||| ||||| |
-gtagctaacgtcacttcttcaacaaacacaaactgatgaaaaattctgagatatgcattctgcattagatccttcaacacacattttgtgt-tctgtgctcagGTAGTTGCTGCTGGAGACTTGTGTGCGATATGCCAAGAAAAGATGCATGTTCCCATCCTTTTGCGCTGCAAACATATCTTCTGTGAAGATTGTGTATCCG
upper sequence: GLYMA18G45010.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0056g00440.t01 (Vitis vinifera), 3'ss of exon 6
agttgtatacttcacagtctgttgttaagagccatat---agccttctatatgcatgtctgggagcagggagttgttcatgcc----tttaatttatctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCTCCCATCTTACTACGTTGTAAACATATTTTCTGTGAAGATTGCGTATCAG
|| | | | | ||||||| |||||| | || || || ||||| | || || | | | | | ||| ||| |||||||||||||||| ||||| || ||||||||||||||||||||||||||||| |||||||| ||||||||||| || || |||||||| || ||||| |
-----catcactagtgctgcatgcctgcttgccatatcacagccttactgttatttg-ctagggcaagggattagtatattctaagatgtcaatggtctaatg-tagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCTCCAATCTTACTTCGTTGTAAACACATCTTTTGTGAAGACTGTGTATCTGMapped 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|8404106|gb|BE059749.1|BE059749EST: CATTGTCGCGTAAAGAAATGCACTATGGGGCTTATGCAACATCAGAGCAG GTCAATGCAGCTGGTGATCTATGTGCTATTTGCCAAGAGAAGATGCATGCT
genomic: CATTGTCGCGTAAAGAAATGCACTATGGGGCTTATGCAACATCAGAGCAGgtacagtggg ... ctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCT
EST:
gi|15814325|gb|BI786600.1|BI786600EST: CATTGTCGCGTAAAGAAATGCACTATGGGGCTTATGCAACATCAGAGCAG GTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCT
genomic: CATTGTCGCGTAAAGAAATGCACTATGGGGCTTATGCAACATCAGAGCAGgtacagtggg ... ctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgcatgtctgggagcagggagttgttcatgcctttaatttatctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCTCCCATCTTACTACGTTGTAAACATATTTTCTGTGAAGATTGCGTATCAG
atctgat putative branch site (score: 4)
tttatct CT-rich tract
tttaatttatctgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttgtatacttcacagtctgttgttaagagccatatagccttctatatgcatgtctgggagcagggagttgttcatgcctttaatttatctgatggcagGTCAATGCAGCTGGTGATCTTTGTGCTATTTGCCAGGAGAAGATGCATGCTCCCATCTTACTACGTTGTAAACATATTTTCTGTGAAGATTGCGTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - acttcac
- - - - - - - - -tctgttg
- - - - - - - - - - - - - - - - - - - - - - - - -gcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgcct