Sequence
atgc intronic sequence ATGC exonic sequence...agcttccatattgatgttgtacctttatgtaaatgatacttgaggagttattactaattactgtaaagattcactattttgactttgttttatggggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGT
Basic information
species | Glycine max |
transcript | GLYMA10G16320.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g46640.1 (Oryza sativa), 3'ss of exon 4
agcttccatattgatgttgtacctttatgtaaatgatacttgaggagttattactaattactgtaaagattcactattttgactttgttttatg-gggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGT
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-tatgcaagtttcaacctaactctatggatgaaccttcattctattattgctagcaaatagctatacaatgcactgacctgacattgtcttccatatgcagGTTCTCTGTACAAGCTCTTTATGCTCCTATTAGCAGTCTTTTGTACAAATTCGATCAATATACATGCTGGCCTGAATGGTCTTGAAGTTGGGCAGACAGT
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G827205_T02 (Zea mays), 3'ss of exon 4
agcttccatattgatgttgtacctttatgtaaatgatacttgaggagttattacta---attactgtaaagattcactattttgactttgttttatggggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGT
| | || | | || | | || || || | ||| | | || | || | ||| || ||||| ||| ||| | ||||| | | || || |||| ||| | || || || ||||| ||||| || || |||||||||||||| ||||||| ||||||||||||||||||||
gaagcctgttctggtttcagctctgtcattgaaccatgtttctgattctataatcagcagctattctacacattgacc-ttttg--tttcctttgtcatgcagGTTTATTTTACAAGCTATTCATGCTCTTGTTAGCAGTCTTTTGTACAAACTCGATAAATATACATGCTGGCCTAAATGGACTTGAAGTTGGGCAGACAGT
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G137707_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------------------agcttccatattgatgttgtaccttt--atgtaaatgatacttgaggagttattactaatta------ctgtaaagattcactattttga--ctttgttttatggggc----agGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGT
| |||| || | | ||| || | | | | | | || || |||| | | | |||| || ||| ||||||| | ||| ||| | | || || |||| ||| | || || || ||||| ||||| || || |||||||||||||| ||||||| ||||||||||||||||| |
gtaggtattgtagataataatctgtcttcagtgtttgtttttgtgaactactattaaaattttccttagctgcatgattacttccaatttcagctctgttgctgaccctgtttctgattatataatcagaagctattctatacactgatcttttgtttcctttggcatgcagGTTTATTTTACAAGCTATTCATGCTCTTGTTAGCAGTCTTTTGTACAAACTCGATAAATATACATGCTGGTCTAAATGGACTTGAAGTTGGGCAGACTAT
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 4
agcttccatattgatgttgtacctttatgtaaatgatacttgaggagttattactaattactgtaaagattcact-attttgactttgttttatggggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGT
| | | || | | || | | || | ||| | | || | || |||| || || ||| ||| ||||| | | || || |||| ||| | || || || ||||| ||||| || || |||||||||||||| ||||||| ||||||||||||||||| |
catgattacttccaatttcagctctgttgctgaccctgtttctgattatataatcagaagctattct-atacactgatcttttgtttcctttggcatgcagGTTTATTTTACAAGCTATTCATGCTCTTGTTAGCAGTCTTTTGTACAAACTCGATAAATATACATGCTGGTCTAAATGGACTTGAAGTTGGGCAGACTAT
upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 4
agcttccatattgatgttgtacctttatgtaaatgatacttgaggagttattactaattactgtaaagattcactattt-tgactttgtttt-atg-gggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGT
||||| | | || | ||| ||| || | || | | | ||| | | ||| || ||| | || ||| | |||||||||| |||||| |||||||||| || |||||||| |||||||| || |||||||||||||||||||| ||||||||||||||||||||||||| ||
agcttgatgaataat-tactacatttgaactgttggttattttgattattgagttgtttatcctttgg--cgactgcttacaactataccttgatgtgaacagGATGGATATATAAATTATATATGGGACTTTTGGCTGTATTTTGCACGAACTCCATCAATATACATGCTGGTTTAAATGGCCTTGAAGTTGGGCAGACTGTMapped 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|193690287|gb|FK631896.1|FK631896EST: TATACCAAAGCCACTTGTCCCACACATTGGGATTGAGGTTTTGGATCTTG GATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATT
genomic: TATACCAAAGCCACTTGTCCCACACATTGGGATTGAGGTTTTGGATCTTGgtaagctttt ... tatggggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATT
EST:
gi|17518507|gb|BM187549.1|BM187549EST: TATACCAAAGCCACTTGTCCCACACATTGGGATTGAGGTTTTGGATCTTG GATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATT
genomic: TATACCAAAGCCACTTGTCCCACACATTGGGATTGAGGTTTTGGATCTTGgtaagctttt ... tatggggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttattactaattactgtaaagattcactattttgactttgttttatggggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGT
ctttgtttt CT-rich tract
ttactaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcttccatattgatgttgtacctttatgtaaatgatacttgaggagttattactaattactgtaaagattcactattttgactttgttttatggggcagGATGGATGTATAAACTATATATGGGGCTCTTGGCTGTTTTTTGCACAAATTCCATCAATATACATGCTGGAATAAATGGCCTTGAAGTTGGGCAGACAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
-gcttcca
- - - - - - gatgttg