Sequence
atgc intronic sequence ATGC exonic sequence...ccaattgatgggtatatggtgaaagtgcctctttatacaatttaagaaaaaaaaatatttatcactattacaaaataatgttggcataatgttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGTGGTATTGGTTCATTGAATTTTGTAATGGGCAATAAG
Basic information
species | Glycine max |
transcript | GLYMA05G21570.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G21570.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g46450.1 (Oryza sativa), 3'ss of exon 5
ccaattgatgggtatatggtgaaagtgcctctttatacaatttaagaaaaaaaaatatttatcactattacaaaataatgttggcataatgttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGTGGTATTGGTTCATTGAATTTTGTAATGGGCAATAAG
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-----------gttagtagagcagtttccattcagaacgttttttaaaaaagaagaattt----------caagctgatgtc----------tatcacagGTTGCAAGCCTTCTACATGATGATGTACTGGATGATGCTGACACTAGGCGTGGCGTCAGTTCGTTGAATTGCATTATGGGGAACAAG
upper sequence: GLYMA05G21570.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G014508_T03 (Zea mays), 3'ss of exon 5
ccaattgatgggtatatggtgaaagtgcctctttatacaatttaagaaaaaaaaatatttatcactattacaaaataatgttggcataatgttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGTGGTATTGGTTCATTGAATTTTGTAATGGGCAATAAG
| | | || || | || ||| | | | | || || | || ||| || | || || | ||||| ||||||||||| || |||||||| || |||||||| ||| |||| |||||| | ||||||||||| | | ||||| || |||
-----------------gttagtattgtggctatcc-----tttagaccacacattgttattctgttttttccctcaatttt--ttttatcttct-gcagGTCGCAAGCCTTCTGCATGATGATGTTCTTGATGATGCTGATACTAGGCGTGGTGTCAGTTCATTGAATCTCATCATGGGGAACAAG
upper sequence: GLYMA05G21570.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G34630.2 (Arabidopsis thaliana), 3'ss of exon 5
ccaattgatgggtatatggtgaaagtgcctctttatacaatttaagaaaaaaaaatatttatca----ctattacaaaataatgttggcataatgttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGTGGTATTGGTTCATTGAATTTTGTAATGGGCAATAAG
|| | | ||| | | ||| ||| | ||| | || || | | | || ||||| | || | || | |||| ||||| || || ||||||||||| |||||||||| ||| | || |||||| ||||||| || ||| |||||||||| || |||
-----------gtgagtaactatagt-tttactcataacattcattaaagatcaagatccagtatcctcccttttaaaatta-gtaatgctcgggtcattgtagGTCGCAAGTCTACTGCACGATGATGTCTTGGATGATGCCGATACAAGGCGTGGTGTTGGTTCCTTAAATGTTGTAATGGGTAACAAG
upper sequence: GLYMA05G21570.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv15s0024g00850.t01 (Vitis vinifera), 3'ss of exon 5
ccaattgatgggtatatggtgaaagtgcctctttatacaatttaagaaaaaaaaatatttatcactattacaaaataatgttggc-ataatgttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGTGGTATTGGTTCATTGAATTTTGTAATGGGCAATAAG
| | | | || | | | | | ||| | ||| | | | ||| | |||| | | | ||||||| ||||||||||| |||||||| |||||||||| || | |||||||||||||||||||| ||| || | ||||||||||||
-ttttagctaaagctgtgaatattcaactataatgtgaacttttcttcttgaggcactttgttatttccttcaaactaagttgtttgtttccctattttagGTGGCTAGCCTTCTTCATGATGATGTCTTGGATGATGCTGAAACGAGACGTGGTATTGGTTCATTAAATATTATGATGGGCAATAAGMapped 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|27424725|gb|CA936245.1|CA936245EST: ATGTACGTTCAAGACAACAACGCATAGCTGAAATAACAGAGATGATTCAT GTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGT
genomic: ATGTACGTTCAAGACAACAACGCATAGCTGAAATAACAGAGATGATTCATgtaagtcctt ... gttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGT
EST:
gi|151411625|gb|EV281436.1|EV281436EST: ATGTACGTTCAAGACAACAACGCATAGCTGAAATAACAGAGATGATTCAT GTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGT
genomic: ATGTACGTTCAAGACAACAACGCATAGCTGAAATAACAGAGATGATTCATgtaagtcctt ... gttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaaaaaaatatttatcactattacaaaataatgttggcataatgttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGTGGTATTGGTTCATTGAATTTTGTAATGGGCAATAAG
aaaaatatttatcact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaattgatgggtatatggtgaaagtgcctctttatacaatttaagaaaaaaaaatatttatcactattacaaaataatgttggcataatgttgtcacagGTGGCAAGCCTTCTTCACGATGATGTACTGGATGATGCAGATTCTAGACGTGGTATTGGTTCATTGAATTTTGTAATGGGCAATAAG
- - -tgatggg
- - - - - - - tatggtg
- - - - - - - - - - - - -tgcctct
- - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttggc