Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtttttgccttttttttcttcttttttaaacccatacgtttatttaatttttttttttttgtggtgcagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA
Basic information
species | Glycine max |
transcript | GLYMA09G40650.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 2
---------------------gtgcgtttttgccttttttttcttcttttttaaacccatacgttt-----atttaatttttttttttttgtggtg-cagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA
| | || |||||| ||||| | || | || | ||| | | |||| || || ||||| ||||| | || || |||||||| || ||||| ||| | || |||||||||||||| || || |||||||| ||||||||||||||||| |||||||
tttcgggcatattattaacttggaaatccttaccttttcattcttgtcgttatgttataagaattatcaggaagtaactcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA
upper sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 2
---------------------gtgcgtttttgccttttttttcttcttttttaaacccatacgtttatt------taatttttttttttttgtggtg-cagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA
| | || |||||| ||||| | || | | |||| ||| | | |||| || || ||||| ||||| | || || |||||||| || ||||| ||| | || |||||||||||||| || || |||||||| ||||||||||||||||| |||||||
ttcgggcatattattaacttggaaattcattaccttttcattcttgtcgtt-atgttagaagaattatcaagaagtaactcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA
upper sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 2
----------------------gtgcgtttttgccttttttttcttcttt-tttaaacccatacg---tttatttaatttttttttttttgtggtg-cagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA
|| ||| | || |||||| | ||| | || | ||| || | |||| | | || ||||| ||||| || | || |||||| |||||||||| ||| ||||||||||||| || || || || |||||||| || |||||||||| || |||||||
tatcatgcttattgctagcctacaaaattattgtgccagtattgttctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
upper sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 2
gtgcgtttttgccttttttttcttcttttt-taaacccatacgtttatttaattttttttt----ttttgtgg-tgcagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA
|| | || || ||| | ||||| ||| | | | || | | | |||||| | ||| | || ||||||||||||| ||| | ||||||||||||||||| ||||||||||||||||| ||||| ||||| || || |||||| || |||||||||| ||||| |
gtaagcttgtgtttttatcttctttctttggtgggttggtgctttgactgatttttttactgggtctttacgtctgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTAMapped 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|18041081|gb|BM309375.1|BM309375EST: CTGTCAAAGTCTTAAACAAAGAGGGTTTACAAGGACATCGAGAGTGGCTT ACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTG
genomic: CTGTCAAAGTCTTAAACAAAGAGGGTTTACAAGGACATCGAGAGTGGCTTgtgcgttttt ... tgtggtgcagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTG
EST:
gi|207774261|gb|GD743719.1|GD743719EST: CGAGAGTGGC-T ACGGAGGNGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTG
genomic: CGAGAGTGGCTTgtgcgttttt ... tgtggtgcagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttcttttttaaacccatacgtttatttaatttttttttttttgtggtgcagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA
atttaat putative branch site (score: 4)
tttatttaattttttt CT-rich tract
ttttttaaacccatac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtttttgccttttttttcttcttttttaaacccatacgtttatttaatttttttttttttgtggtgcagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT