Sequence
atgc intronic sequence ATGC exonic sequenceTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctggaatatgatattctaatctagtcagta...
Basic information
species | Glycine max |
transcript | GLYMA03G41180.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 10
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtt-tgtcttt--caattttttttttctact----gattgtttgcccttgtattatgt-----tgatgagaagtcacatta------gctggaatatgatattctaatctagtcagta---------------------------------
||| ||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||| ||| | |||||||| ||||| ||||||||||| ||||| |||| || || || | | | | |||||| || |||| || |||| | | || | || | | | ||| || | |||| ||
TTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAAGAACCTGTGCTTTTTGAGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagcatcttggacagaattattgatgcattttaggcctgtttggaacagtggaatgtcagcatgttgaggaattgcaccatttaatgcaaaattcctgtgttccaaacaagtccttaaactgaatttgataaatcttttcttttccacag
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 10
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctggaatatgatattctaatctagtcagta
||| || |||||||||||||| ||||||||||||||||| ||||| |||||||||||| ||| ||| | |||||||| ||||| ||||||||||| ||||| | | | | || | || || | || |||| || || | |||
TTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAAGAGCCTGTGCTTTTTCTGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagattctcatacatattacataaacgttttatctgggcttgataaatatt--ttcctttctacag---------------------------------
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 5'ss of exon 9
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtt--------tgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctgg-aatatgatattctaa-tctagtcagta-------------------------------------
|||||||| ||||| |||||| |||||||||||||||| ||||| |||| ||||| |||||||| | || ||||| ||||| ||||| |||||||||||| ||||| | |||||| |||||| ||| | | ||| | | | |||||| | | | | | | |||| | ||| | | |
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatgtctcttgtttttttctttctat--attaag-gaagatatatgacagtcac-agaagtagtttgggttcccagtttttctttctgactcttgcgattttgtcttgtgtttgattgttttttatttccttccacag
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtt--------tgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgag---aagtcacattagctggaatatgatattctaatctagtcagta---------------------
|||||||| ||||| |||||| |||||||||||||||| ||||| |||| ||||| |||||||| | || ||||| ||||| ||||| |||||||||||| | ||| | ||| || |||||| | || | | | ||| || | | | || | | |||| || | | | | |
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatatctcttgttttcttctttctatatttagtatagtcacagaagtagtttgtgttcccagttttctttctgagtcttgtgattttgttttgtgtttgattgttttttatttccttccacag
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S7_163V6.1 (Physcomitrella patens), 5'ss of exon 10
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaatt-ttttttttctactgattgttt-gcccttgtattatgttgatga-gaagtcacatta--gctgg--aatatgatattct------aatctagtcagta------------
|||||| ||||||||| | ||||| |||||||||||||| || || ||||| |||||||||||||| | || || || | || ||||| ||||||| || | ||| | | | | || | | || ||| || | || | || | | | | | ||| | | ||| | ||| ||| || | || || | ||
TTTTTACGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGACAGATATGATCGGACCTGCTgtaagcgtttgagtagtctcttctacattggttgcttcactattcgactaaatgggtctcgcattcatttcactgctagttaatgtgaagttttcactgaaacttatcctctactctggctgcag
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S191_94V6.1 (Physcomitrella patens), 5'ss of exon 11
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtt--------tgtctttcaatttttt----------ttttctactgattgtttgcccttgtattatgttgatgagaa-gtcac----attagctggaatatgatattctaatctagtcagta-----
|||||||||||||||||| ||||||||||| || ||||| |||||| | | | ||||| || || | || || || ||| ||||| |||| |||| || ||| ||| || || ||| | | | || || ||| ||||| | | || || || ||| |||| | | || || | | || ||
TTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAAGAAGCAATTTTATTTGAAGACATTGTTTGTCAAATGTGTGATATGATCAAACCTAAGgtaattttgcatggatttagattgattgtgtgcataattacctaatattagagagcttttaaattttgttgctaaaaaagttactaggattttatggattcttatgtttc--ttttgttggtttacag
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctgga----atatgatattctaatctagtcagta-------------------------------------
|||||||||||||||| | ||||| |||||||||||||| || || ||||| |||||||||||||| | || || || |||||||| ||||||| ||| ||| || ||| || | | | || | | | | ||| || | | ||| ||| || | |||
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattct--gaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ32791 (Selaginella moellendorffii), 5'ss of exon 10
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctggaatatgatattctaatctagtcagta
||||||||||||||||||||||| ||||||||| | || ||||| || || || || ||||| ||| | |||||||| | |||||||| | || ||||| || || | || | | || ||| | | | | ||| |
CTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAAGACCCCGTCCTCTTCGAGGACATAGTCTGCCAGATGACGGACATGATCTGCCCAGAGgtgcgttagctgtttgtagcttccgggctctcgtcaatgcttatgtga--tcgattgcag----------------------------------------
upper sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ20642 (Selaginella moellendorffii), 5'ss of exon 10
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctggaatatgatattctaatctagtcagta
||||| ||||||||||||||||| ||||||||| | || ||||| || || || || ||||| ||| | |||||||| | |||||||| | || ||||| || || | || | | || ||| | | || ||
CTTTTACGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAAGACCCCGTCCTCTTCGAGGACATAGTCTGCCAGATGACGGACATGATCTGCCCAGAGgtgcgttagctgtttgtagcttccgggctctcgtcaatgcttatgtgat-ccattgcag-----------------------------------------Mapped 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|17023595|gb|BM094629.1|BM094629EST: TGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAG GAAGAGAGCTATATAACTCTGCGTGACCTGAAAGGTGGTAAACTCTCAGGA
genomic: TGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtcttt ... cactctgcagGAAGAGAGCTATATAACTCTGCGTGACCTGAAAGGTGGTAAACTCTCAGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctggaatatgatattctaatctagtcagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT