Sequence
atgc intronic sequence ATGC exonic sequencegtaagttattaatttgctatttttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
Basic information
species | Glycine max |
transcript | GLYMA13G36570.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 5
-------gtaagttattaatttgctatttttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
|| || | || ||| | ||| | ||| ||| | || | | || | | |||||||||| ||||| || ||||||||||| ||||| ||||| |||||||| ||||||
gtatgacttatgtgaacaaggctacattacttctcttgcttggttgtttgttttgaactggtctctaattgcttgctgatacagGTTGATCCTCTCACTCATCAAGTCAAGCTATGTGACTTTGGAAGTGCAAAGGTTCTG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 5
------gtaagttattaatttgctatttttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
| | || | || |||||| | | | | || ||| ||||| | | ||| | |||| ||||| || || || ||||||||||||||||| |||||||| |||||| |||
gtaggtattcatgatcagattattattttgct--atgcgatggcctttgattattggctctgaactcctttcttgcaatacagGTGGATCCTCTAACTCATCAAGTCAAGCTCTGTGACTTTGGGAGCGCAAAAACACTG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 5
-------gtaagttattaatttgctatttttcctcaaggagttgcatttatttatta--taaacctattgtccat--ttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
| || || | || ||||| | | | | ||| || | | | | | ||| | ||| | | |||||||||| ||||| ||||| |||||||||||||| ||||| |||||||||||||||
gtatgtgtcatgtggacaaggatttgttcttccttt-gatttggtaattagttctgaattggtctcgtcgtctctctttgatgtacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGTGCAAAAGTTCTG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 5
-------gtaagttattaatttgctatttttcctcaaggagttgcatttatttatta-taaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
| || || | || || || | | | | || || | | | || | |||| | | |||||||||| ||||| ||||| |||||||||||||| ||||| || |||||||| |||
gtacgtgtcatgtggacaaggtttcgttctttcttt-gatttggtaactagttctgagttggtctgatccttctttgatatacagGTTGATCCTCTCACCCACCAGGTCAAGCTCTGTGACTTTGGTAGCGCAAAAGTCCTG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtt-attaatttgctatttttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
||| ||| || ||| |||| || | | || ||| ||| | |||| || | |||||||||||||||||| ||||| || || ||||||||||||||||| ||||||||||| |||
gtacgttgatctattgtgggttttgtctttggtaaccttgacta--gattgtaatcttattctctgtatgttctgtagGTTGATCCCCTCACCCATCAGTGTAAGCTCTGTGATTTTGGAAGTGCAAAAGTACTG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 5
--------------------gtaagttattaatttgctatttttcctcaaggagttgcatttatttattataaacct-attgtccatttgttc-----tgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
||| | | |||| | |||| | ||| || || | | ||| |||| | || |||||||||| ||||| || || || ||||| ||||||||||| |||||||| ||||||
gtatattgttcattttttgataaagattatggcatgctgaatcccctccccttcccccctttcctttaaatgacttggactgtttctttgaacataattgcagGTTGATCCTCTCACCCATCAGGTTAAGCTTTGTGATTTTGGAAGTGCAAAGGTTCTG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttattaatttgctatttttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
|| | || | | | || || | | ||| | | | | || ||| |||| | |||| |||||| ||||||||| ||||||||||||| ||||||||||| ||||| ||
----gtaa--aaccctccttgtgctttcgagtcctggaattcttatgcttt---tcttttgctggtttg--catcagGTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTG
upper sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 6
gtaagttattaatttgctatttttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
| || | | | || || | | ||| | | | | || ||| | ||| |||| |||||| ||||||||| ||||||||||||| ||||||||||| ||||| ||
-------gtaaaccctccttgtgctttcgagtcctggaattcttatgcttt---tcttttgctggat--ttcatcagGTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTGMapped 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|17402010|gb|BM178792.1|BM178792EST: ACACTGTACCAGGAATTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTA GTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAA
genomic: ACACTGTACCAGGAATTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTAgtaagttatt ... tgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
tttgttct CT-rich tract
atttatttattataaa 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
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gtaagttattaatttgctatttttcctcaaggagttgcatttatttattataaacctattgtccatttgttctgtagGTTGATCCACTCACACACCAAGTCAAGCTCTGTGATTTTGGGAGTGCAAAAGTTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT