Sequence
atgc intronic sequence ATGC exonic sequence...gaaagagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaatattgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC
Basic information
species | Glycine max |
transcript | GLYMA12G01200.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G01200.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 5
gaaagagctccttttaaagcacagtaaatacatgct--tgattcttgtcaattaatattgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC
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-----------------------gttagttcattctattaactttatttggtttccatcggtctgaagtcctgtgctaatgccaaccttcctt--tttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC
upper sequence: GLYMA12G01200.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G162251_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------------------------gaaagagctccttttaa--agcacagtaaatac--atgcttgattcttgtcaattaatat---tgtattgttggtaaatggtgagactgttgttggttcat--atgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC
| ||| |||| |||| || | | | | | ||||| | | || || | | || || | | | |||| |||||||||| ||||||| ||||| ||| ||| | | |||||||| | ||||| ||||||||||||| ||||||||||| || ||||| ||||| |||||
gtatgcactgaagcactatttacttatcttaatattttattcatcatgcaacccctttattaactcttcttttctcctggcaccatgtaaatgaagcagattttggacagcaaggtcagcgtcaacgaatcaactttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC
upper sequence: GLYMA12G01200.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G162251_T02 (Zea mays), 3'ss of exon 4
gaaagagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaatattgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC
| | | || ||| | ||| | || || || | | | | ||| | | | || |||||||||| ||||||| ||||| ||| ||| | | |||||||| | ||||| ||||||||||||| ||||||||||| || ||||| ||||| |||||
------------gtcagcgt-caacgaatcaa--ctttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactat-tgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC
upper sequence: GLYMA12G01200.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G30700.1 (Arabidopsis thaliana), 3'ss of exon 5
gaaagagctccttttaaagcacagtaaatacatgcttgattcttgtcaat-taatattgtatt--gttggtaaatggtga-gactgttgttggttcata-------tgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC
|| || | || | | | | || ||||| ||| | | | | ||| || || | | || || |||| | | | | |||| ||| | || |||||| |||| || |||||||||| || ||||||||| ||||||||||||||||||| || ||||||||||| || |||||
-gtttgcatcaattcatctcatattccaaagttgtttgatatgtgttgttgtctcgccagaataagttaaaaagtgttaatgatcttttttgggtaacaatgtgattatagGTTGTCTTCTGAGAAGCTATCCTGCAGACTTGATATTTGATAACACATCAGGCTACAGCTTTACATGTGATTTGACAGACAACATTGCTGCTCCATGGCC
upper sequence: GLYMA12G01200.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0094g00050.t01 (Vitis vinifera), 3'ss of exon 3
-gaaagagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaatattgtattgttggtaaatggtgagactgttgtt-ggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC
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tccagtaactcctttgaaaatgccatgttttagtgtatg--ccaaattaaatatttgtttgggtctgtagaagaaatgaactgtggtcaggtttaaatgcagGATGTCTACTTCGAAGCTTGCCTGCAGATGTGGACTTTGACAATTCAACAGGCTTCAGCTTTACGTGTGACTTGAGTGATAATATTGCAGCTCCATGGCCMapped 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|51343854|gb|CO984587.1|CO984587EST: AGCATACAAGCTTATGGACAACAAG GCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgccctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAG
EST:
gi|208216244|gb|GE009362.1|GE009362EST: AGCATACAAGCTTATGGACAACAAG GCTGTTTACTTCGAAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgccctt ... tcatatgtagGCTGTTTACTTCGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaattaatattgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC
aattaat putative branch site (score: 3)
taatattgtattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaagagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaatattgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - -agctcct
- - - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttg