Sequence
atgc intronic sequence ATGC exonic sequence...aacagtcaaagatgttaatgctggactgttgagtttgtgtattgccattgtgcaataggtgttgtctgtgttggttgatgttgagtttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
Basic information
species | Glycine max |
transcript | GLYMA10G25630.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 3
aacagtcaaagatgttaatgctggactgttgagtttgtgtattgccattgtgcaataggtgttgtctgtgttg-gttgatgttgagtttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
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-gttatgtgagattgcttttttagttttttatggatctttaacagtacattttgggagttatcatgcaaacaatgttgagctcaatataactatgttgcagGGACGCACTGTTGTTATTGAGCAAAGCTTTGGTGCTCCTAAAGTTACAAAGGATGGAGTTACTGTTGCCAAGAGCATTGAATTCAGTAACAGGGTTAAGA
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 2
aacagtcaaagatgttaatgctggactgttgagtttgtgtattgccattgtgcaatag-gtgttgtctgtgttg-gttgatgttgagtttattctcttt-tagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
|| ||| ||| |||| || || || | || | || | || | | | | | || ||| ||| | || | | | || | | ||||||| ||||| || ||||||||||| |||||||| || ||||| || || ||||| || ||||| ||||||||||||||||| ||||||| ||| ||||
-gcactcactgattataatattgc-ttgatgtgctt-tactctgttgtagtactgttgcatttagtttgttttgtacttgaatttattgcctgctttctgcagGGGCGCAATGTGGTTATTGAGCAAAGCTTTGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 2
aacagtcaaagatgttaatgctggactgttgagtttg-tgtattgccattgtgcaataggtgttgtctgtgttg--gttgatgttgagtttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
| ||| ||| ||| ||| ||| ||| | | ||| || || ||||| ||| ||| |||| || || | |||||||| ||||| || ||||||||||| || ||||| || ||||| || || ||||| || |||||||| |||||||||||||| ||||||| ||| ||||
---actcactgattccaatactgtttggtttgttttactttgttgtaatactgttgccttagttgtttgttttgtacttgaacttatcgcctgccttctgtagGGGCGCAATGTGGTTATTGAGCAAAGCTTCGGTGCACCGAAAGTCACAAAGGATGGTGTGACTGTTGCGAAGAGCATTGAATTTAAGGATAGAGTAAAGA
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------aacagtcaaagatgttaatgctggactgttgagtttgtgtattgcc-attgtgcaataggtgttgtctgtgttggttgatgttgagt--ttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
| || || | | | ||| | ||| | ||| || | | | |||| | | || || || | | || |||| ||||||||||||||||||||||||| ||||| |||||||| || |||||||| || |||||||| || || ||||| ||||| || ||| ||||||
gtactctttttcttctacacattttgatttgatttggacatgatttggccagaggttccttccttagcatgtgatttgggtgaccggttgattctgtatcgaatttggtctaagactttctgctttatgtgattctaattttgaagGGACGTAATGTTGTGATTGAGCAAAGTTGGGGTGCTCCTAAAGTGACAAAAGATGGTGTTACTGTTGCCAAAAGTATTGAGTTCAAAGACAAAATTAAGA
upper sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------aacagtcaaagatgttaatgc----tggactgttgagtttgtgta---ttgccattgtgcaataggtgttgtctgtgttggt-tgatgttgagtttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
|| |||| ||| | | || | | ||| | ||| | | || | || |||| || ||| |||| | | | || |||| || | |||| | || |||||| |||||| | |||||||| ||||| ||||| || |||||||| || ||||||||||||||||| | ||||||
gtaacctgctgcctgctattttgcttttcagtagggatcaatcccgaactgtctaattcttggtattctagctttagatccgagattttactttgacttagagtcgtagttttagggggatttgataacatagtttacgaattaactgtaatgtcgtgacgttgtgctctctttccaacagGGCCGGACTGTTATCATCGAGCAATCTTTTGGATCTCCTAAAGTGACCAAGGATGGTGTTACTGTTGCGAAAAGCATTGAATTCAAGGACAGGCTTAAGAMapped 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|192326682|gb|FK018869.1|FK018869EST: AGGGTGTTGAAGAGCTAGCTGATGCTGTCAAAGTAACCATGGGTCCCAAG GGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAA
genomic: AGGGTGTTGAAGAGCTAGCTGATGCTGTCAAAGTAACCATGGGTCCCAAGgttatctttt ... tctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAA
EST:
gi|16276997|gb|BI942150.1|BI942150EST: AGGGTGTTGAAGAGCTAGCTGATGCTGTCAAAGTAACCATGGGTCCCAAG GGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAA
genomic: AGGGTGTTGAAGAGCTAGCTGATGCTGTCAAAGTAACCATGGGTCCCAAGgttatctttt ... tctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattgtgcaataggtgttgtctgtgttggttgatgttgagtttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
ggttgat putative branch site (score: 5)
tttattctctttt putative PPT
tttattctctttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacagtcaaagatgttaatgctggactgttgagtttgtgtattgccattgtgcaataggtgttgtctgtgttggttgatgttgagtttattctcttttagGGGCGTAATGTTGTGATTGAGCAAAGTTTTGGTGCCCCTAAAGTAACCAAAGATGGAGTAACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - tgctgga
- - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - gtttgtg
- - - - - - - - - - - - - - - - - - - -tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - tgtgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgttg