Sequence
atgc intronic sequence ATGC exonic sequence...ataagaacactgtttcatggtttatgggagcttacattaaacttacgctaacattcaatccattttggacaatattttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
Basic information
species | Glycine max |
transcript | GLYMA09G02490.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g41170.1 (Oryza sativa), 3'ss of exon 4
-----------------------------ataagaacactgtttcatggtttatgggagcttac---attaaacttacgctaacattcaatccattttg-gacaatattttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
| || || | | | || | ||| | | || ||||| | | | ||| | || ||| | | || | | | | | |||||||| ||||||||||| || |||||||| || ||||| |||||| |||||||||| ||||||
gtgagttactcaattgttcaactctactactgagctcatattatgaaaattcctcatagccttctaggttgaactttaatatataattcatcaacttcatgactttgtattaccaccatatgtatgtcgatagGTGGTGCCATGATATTGGCCGGGAACAAGCTGCCAATAAGCCTCTTCTAAAAACAGTATTTCAG
upper sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G390374_T01 (Zea mays), 3'ss of exon 4
ataaga-acactgtttcatggtttatgggagcttacattaaactta--cgct-aacattcaatc----cattttggacaatattttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
| || || |||| | || | | | ||| | | ||| ||||| | | ||| || | | || | || ||||| | | || | | |||||||||| ||||||||||| || |||||||| || |||||||| ||| |||| || || ||||||
gtgagtcaccctgtatgatattgt-tacgagttccccttagacttatttgttgaacctttagttatcacactacatacttaattttatctctatgtttatgtgtacagGTGGTGCCATGATATTGGCCGTGAACAAGCTGCCAATAAACCACTTCTAAAGACTGTATTTCAG
upper sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0116g00810.t01 (Vitis vinifera), 3'ss of exon 3
ataagaacactgtttcatggtttatgggagcttacatta-aacttacgctaacattcaatccattttggacaatat---tttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
| || ||| | || | | || || | | ||| | | || | | | || |||| | | || || | | |||||||||| ||||||||||||||||| || || || || ||||||||| | ||||||||||| |||
----aatcatgagatcaagagtttcgcagacataaatggcgggtgatgctcagggtatattgttatagaactatatgagcattgaatttgaatatctattacagGTGGTGCCATGATATTGGTCGAGAGCATGCTGCGAACAAACCTCTTCTGAAAACAGTTTTCCAG
upper sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ31796 (Selaginella moellendorffii), 3'ss of exon 5
ataagaacactgtttcatggtttatgggagcttacattaaacttacgctaacattcaatccattttggacaatattttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
|| || || | | || ||| || || || || ||| | | |||||||||||||||||||||||||| || ||||| || |||||| | | || || || ||||||
-------------------------------------gtaagttgttgtagtacttcgtctgttt------atgttcgtcag----tactttcgtaa-agGTGGTGTCATGATATTGGTCGAGAGCACGCAGCCAACAAACCTTTGCTGAAGACCGTCTTTCAG
upper sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ38064 (Selaginella moellendorffii), 3'ss of exon 4
ataagaacactgtttcatggtttatgggagcttacattaaacttacgctaacattcaatccattttggacaatattttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
||| | || || | | || ||| || || || || ||| | | |||||||||||||||||||||||||| || ||||| || |||||| | | || || || ||||||
------------------------------------gtaagttgtcg-tagtacttcgtctgttt------atgttcgtcag----tactttcgtaa-agGTGGTGTCATGATATTGGTCGAGAGCACGCAGCCAACAAACCTTTGCTGAAGACCGTCTTTCAGMapped 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|17023193|gb|BM094227.1|BM094227EST: CAGAGTGCTCTTTTTGCTTTGGCAATATCAGATATTGTTCTGATAAACAT GTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAA
genomic: CAGAGTGCTCTTTTTGCTTTGGCAATATCAGATATTGTTCTGATAAACATgtaagttttt ... ttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAA
EST:
gi|209698106|gb|BW661049.1|BW661049EST: CAGAGTGCTCTTTTTGCTTTGGCAATATCAGATATTGTTCTGATAAACAT GTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAA
genomic: CAGAGTGCTCTTTTTGCTTTGGCAATATCAGATATTGTTCTGATAAACATgtaagttttt ... ttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctaacattcaatccattttggacaatattttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
ttttatttt CT-rich tract
attttggacaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataagaacactgtttcatggtttatgggagcttacattaaacttacgctaacattcaatccattttggacaatattttgaagattttattttattcacagGTGGTGTCATGATATTGGTCGAGAACAAGCAGCAAATAAACCTCTTTTAAAAACAGTTTTTCAG
- - - - - - -ttcatgg
- - - - - - - - - - - - - - -gcttaca
- - - - - - - - - - - - - - - - - - - - - - - - - acattca