Sequence
atgc intronic sequence ATGC exonic sequence...tttaattctattcctttcctaatgctagaaatatttcttcacagcaacatttgagctaggagtttacccacttattatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG
Basic information
species | Glycine max |
transcript | GLYMA18G50960.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g21780.1 (Oryza sativa), 3'ss of exon 4
tttaattct--attcctttcctaatgctagaaatatttcttcacagcaacatttgagctaggagtttacccacttattatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG-
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tgtaattgtgcattatcttttcaatttcaatatcacacacacgcacaaaggtctcatcttt---tcctgatagctctgttgtctgtttgctgcattattttagCTCGATGTTTGGGCGAAGGAAAGAGAAGTTGCTGGGTTAAAGGCAAGCTTGAATACACTGACTTCTGAGGTACAGCGTCTGTACAAGTTATGTGCTGAGT
upper sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G055917_T02 (Zea mays), 3'ss of exon 4
tttaattctattcctttcctaatgctagaaatatttcttcacagcaacatttgagctaggagtttac-ccacttattatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG-
||| | | | ||| | | | | | || || | |||| | | | | || || | | || | | | || |||| ||||||||||||||||||||||||||||| || ||||||||||||| | || | | ||||| ||||||| ||| ||||||| |||||||||
-ttagctttttaattttgcaattttcttattcaatttagcata-taacaaaaaaagggataatcaataccttttcctgataacatagtctacctcattttagCTGGATGTTTGGGCCAAGGAAAGAGAAGTTGCAGGACTAAAGGCAAGCTTGAGTACACTTACATCTGAGGTACAACGTTTGTATAAGTTATGTGCTGAGT
upper sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G116196_T01 (Zea mays), 3'ss of exon 4
----tttaattctattcctttcctaatgctagaaatatttcttcacagcaacatttgagctaggagtttacccacttattatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG-
||||||||| | ||| || || | | || | || | || |||| | | | || || | || | | || | | || || | || |||||||||||||||||||||||||| || ||||||| ||||| | || | | ||||| ||||||| ||| ||||||| || ||||||
gctctttaattctg--cattttcttattcaatttatcatataacaaaaaaaactttggatgatcaat--acttttttgtgataacgtagtctacctcat-tttagTTGGACGTTTGGGCCAAGGAAAGAGAAGTTGCAGGACTAAAGGCGAGCTTGAGTACACTTACATCTGAGGTACAACGTTTGTATAAGTTATGCGCTGAGT
upper sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G38880.1 (Arabidopsis thaliana), 3'ss of exon 4
--tttaattctattcctttcctaatgctagaaatatttcttcacagcaacatttgagctaggagtttacccactt-attatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG-
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actgcatgactgattctcagttatcattaaagttcattttatgtt-taatatatatgctga---tttacttgcttgaacaaacgatccgattttatctttgcagTTGGATGTATGGGGAAAGGAAAGAGAAGCTGCTGGTTTGAGGGCTAGCTTAAACACATTGTTATCTGAAATACAACGGCTGAATAAATTATGTGCAGAAAMapped 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|22522696|gb|BU081507.1|BU081507EST: CTTGGTATTGGAAGTAATTCCCAAAATGTTGGAAGTCTCAGGCAATTTTA GCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTT
genomic: CTTGGTATTGGAAGTAATTCCCAAAATGTTGGAAGTCTCAGGCAACTTGAggtattatta ... cacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTT
EST:
gi|208109768|gb|GD905372.1|GD905372EST: CAGGCAACTTGA GCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTT
genomic: CAGGCAACTTGAggtattatta ... cacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatttgagctaggagtttacccacttattatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG
tattttttcc CT-rich tract
acttattatgtatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaattctattcctttcctaatgctagaaatatttcttcacagcaacatttgagctaggagtttacccacttattatgtatattttttccacgtgttcaGCTAGATGTTTGGGCCAAGGAAAGAGAAGTTGCTGGTTTAAAGGCAAGCTTAAACACCTTAATGTCTGAAATACAACGCTTGAATAAGTTGTGTGCTGAG
- - - - - - cctttcc
- - - - - - - - - - aatgcta
- - - - - - - - - - - - - - - - - -tcttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacccac