Sequence
atgc intronic sequence ATGC exonic sequence...tctatcattggtagaacaagaactcaaaactattgctgtatatttttatgtttggattttgtccttttttatttatgttctcatgtggaaattaatgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
Basic information
species | Glycine max |
transcript | GLYMA01G04930.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 3
tctatcattg-gtagaacaagaactcaaaact--attgctgtatatttttatgtttggattttgtccttttttatttatgttctcatgtggaaatta----atgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
||| || || | | | | ||| | ||||| | ||| | || | | | | | ||| | || || | | |||| | ||| || | ||||| |||||| |||| ||||||| ||| ||||| || ||||||||||| ||||||||||||||||||||||||||| | ||||| || ||
------gttgcgttaaatttggcccaactgtttcatttcagtataactctat-tctgaagtgtcttgtatttatctgatatttgtcttggataattgtattaaacagGGTCTTTACCTCTCCCATGGGCCATCAGAATGAGAATAGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------------------------tctatcattggta---gaacaagaactcaaaactattg---ctgtatatttttatgtttgga------ttttgtccttttttatttatgttctcatgtg----gaaattaa--tgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
||||||| || || | || || | || | | || || || | | | || | | || | ||| || || ||| | | |||| || | ||||| || |||||||| |||||||| |||| || ||||| || |||||||||||||| |||||||||||||| ||| ||||||| || ||
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcattcatatttgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatagatagaaatattgaatcttatatgatttatgattcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 3
tctatcattggtagaacaagaactcaaaactattgctgtatatttttatg----tttggattttgtccttttttatttatgttctcatgtggaaattaatgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
| ||| | | | | | | | | ||| | | | || | || ||| | || | | | || | | | || || ||| || ||||||| |||||| ||||||||||||||||||| || || ||||| || || || |||||||||||||||||||||||| |||||||||| ||
---aggattttatgtgctaaatttgaccagtgttgttttgttttgtcataacatcttgaaccttcacatacccatctaataacattttttttgtatcaa-atagAGTCATTGCCTCTACCATGGGCCATTAGAATGAAAATTGCTCTTGGTGCTGCGAAAGGCCTCGCTTTTCTTCATGAAGAAGCTGAAAGACCAGTAATCTA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------tctatcattggtagaacaagaactcaaaactatt--gctgtatatttttatgtt-------tggattttg--tccttttttatttatgttc--tcatgtggaaattaatgt------------agGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
||| | | | || || | | ||| ||| | ||| ||| || |||| | | | | ||||| || | | |||| | ||| ||| || | ||||| |||||| | || |||||||| ||||||| ||||| || |||||||| ||||| |||||||||||||| ||| ||||||| || ||
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G150806_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------tctatcattggtagaacaagaactcaaaac-tattgctgtatatttttatgt---ttggat----tttgtccttttttat-------ttatgttctcatgtggaaa----------ttaatgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
||| | | | || | || | | | |||||| | ||| ||| || | ||| | | || || | | | || | | || |||||| || | ||||| |||||| | || |||||||| ||||||| ||||| || |||||||| ||||| |||||||||||||| ||| | ||||| || ||
gtatgtatctggcttattccttaatgattggagcactaacttctgtttaggattcacctttttttcttaagcaaataatcgtgtatcatatgagggcgcatgatgttctcctgtatttatttgtgtagcttaggcatcctttaaatagtatcatggaaatgttgaatcttaaagtaaacaattctgctttctactgtagGGTCTCTTCCTCTCCCATGGGCTATCAGAATGAAGGTTGCACTGGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGTCCAGTCATTTA
upper sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
tctatcattggtagaacaagaactcaaaactattgctgtatatttttatgtttg-gattttgtccttttttatttatgttctcatgtggaaatta------atgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
|||| | | | | | |||| | | | |||| || | | ||||| ||||| || || || | ||||||| || |||||||||||||| |||| || ||||||||||||||||| ||||||||||||||||| ||||||||||| ||||| ||| | ||||| |||||
-------atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgttttctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATAMapped 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|15285775|gb|BI469666.1|BI469666EST: AGTGTATGAATTCATGCCTCGGGGTAGCCTGGAAAACCACTTATTTAGGA GATCCATGCCCTCT-CCATGGTCCATTAGAAATGAAA-TTGCACTAGGAGC
genomic: AGTGTATGAATTCATGCCTCGGGGTAGCCTGGAAAACCACTTATTTAGGAgtaagttact ... attaatgtagGATCCATGCC-TCTTCCATGGTCCATTAGAA-TGAAAATTGCACTAGGAGC
EST:
gi|207771334|gb|GD746449.1|GD746449EST: AGTGTATGAGTTCATGCCTCGGGGTAGCCTGGAAAACCACTTATTTAGGA GATCCATTCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTG
genomic: AGTGTATGAATTCATGCCTCGGGGTAGCCTGGAAAACCACTTATTTAGGAgtaagttact ... attaatgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtttggattttgtccttttttatttatgttctcatgtggaaattaatgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
aattaat putative branch site (score: 3)
attttgtcctttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctatcattggtagaacaagaactcaaaactattgctgtatatttttatgtttggattttgtccttttttatttatgttctcatgtggaaattaatgtagGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - agaacaag
- - - - - - - - - - -actcaaa
- - - - - - - - - - - - - - - - -tgctgta
- - - - - - - - - - - - - - - - - - - - - - - -atgtttg