Sequence
atgc intronic sequence ATGC exonic sequence...ggaaaagtaagaacaccaagtggctgaaattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAAGCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
Basic information
species | Glycine max |
transcript | GLYMA04G36360.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 7
------------------------ggaaaagtaagaacaccaagtggctgaaattg--ctatgctattaggtca-gatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
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gtatactttgttcttctacctatttgaccttttagcctttttaacgtcttctttttacccggtttagctgattatgattcaacaattttatgttatctttctaatccttcta--caatctctgctagGTTTCATCCCGTTCTCCAAAGGAAGGTTCCTATTTCAAGCAGCTGCCCAAGTCCAGTGCTATTAAGGTGATTGATTTTGGCAGCACAACATATGACCAGC------
upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G179308_T04 (Zea mays), 3'ss of exon 3
------ggaaaagtaagaacaccaagtggctga-aattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
|| | | | || ||| || ||| || | || ||||| || ||| ||| | || | || | | || ||| |||| || | || || |||| |||| | |||| || |||| | ||||||||||| |||||||| || || ||||||||||| |||||||| ||||| | |
acctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttagt----gaatattgaata-tggtactgat--cctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 6
--------------------------------ggaaaagtaagaacaccaagtggctga-aattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
|| | | | || ||| || ||| || | || ||||| || ||| ||| | || | || | | || ||| |||| || | || || |||| |||| | |||| || |||| | ||||||||||| |||||||| || || ||||||||||| |||||||| ||||| | |
gtatattttgttcttttatttacatcacctacccaagatttaccttgccctgtgcttgttgatttctgttgtaataggttagt----gaatattgaata-tggtactgat--cctctttttttcatttgctagGTTTCATCCCGATCCCCAAAGGAGGGATCCTATTACAAGCGGGTGCCCAAGTCTAGTGCTATCAAGGTGATTGATTTTGGTAGCACTACCTATGATCAAC------
upper sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 7
-----------ggaaaagtaa-gaacaccaagtggc---tgaaattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAA------GCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
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gtactccagatgttaacttgatgtgtattaagtggcatatggttttgctttattattctttctgcatctacaatgcccttgttattgt--aacatatatttgttgcatttt-cagGTTTCATCCCGTTCACCCAAGGATGGTTCTTACTTTAAGAGAGTACCAAAATCAAGTGCTATTAAAGTGATTGATTTTGGAAGCACAACATATGAGCGAC------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|58021621|gb|CX708362.1|CX708362EST: AAAACATACTTTTAGTTTCACCAGAGTATCTTAAGATTCCTGANTACAAG AGTACAACCAGATCACCAAGCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGT
genomic: AAAACATACTTCTAGTTTCACCAGAGTATCTTAAGATTCCTGACTACAAGgtacacttgt ... tatttaacagAGTACAACCAGATCACCAAGCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAAGCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
cactgac putative branch site (score: 2)
attgcttattgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaaagtaagaacaccaagtggctgaaattgctatgctattaggtcagatacagaaatgtgatcactgacatccattgcttattgtttatatttaacagAGTACAACCAGATCACCAAGCTCCTTTTTCAAGAGAGTGCCCAAGTCAAGTGCTATAAAAGTTATTGATTTTGGCAGCACTACATATGAACGAGAAGATC
- aaaagtaa
- - - - - - acaccaa
- - - - - - - - - - tggctga
- - - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttat