Sequence
atgc intronic sequence ATGC exonic sequence...cattttgtttaaaaaatattggagatagaataatatcatttctttctagtgttcacttttccttgaatgaaagtcaactgctttttgttttgatttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
Basic information
species | Glycine max |
transcript | GLYMA07G09750.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g45840.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------cattttgtttaaaaaatattggagatagaataatatcatttctttctagtgttcactttt------ccttgaatgaaagtcaactgctttttg--ttttgatt----tatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
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gtaagtggtgaaaatatccttctagtgtttcctctgtttcttactttaaaaatgcaattccacaactacttgtgattgactatgacaattatgaatttatgtgcagaagtaataaactcctgataaatgttgtctaattactgaactttaattattcttcagTCGGGAGTTCACTCATCGTGTAAAATCAATATCAATGGCTAAATTTACTTCTCAAGAAGTTTCTGCTCTTCAAGAAGGGGGAAACGAG
upper sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g11820.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------cattttgtttaaaaaatattggagatagaataatatcatttctttctagtgttcacttttccttgaatgaaagtcaactgctttttgttttgatttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
| | | || | | | | | || ||||| | ||| | | || || | | ||| ||||||||| || ||| || || ||||| ||||||| || |||||||| |||||||| |||||| |||| ||||||||||| |||||||||||||| ||| ||
gtaagattcttattcagttctgttttgttacacttgtaatatgtcgaacctctctagcttcactgtccctttggtcaaattagatgcattttagtgaagtcagtgatcctaattttattgatgacaaaa----tttgttttgcttc-tagCCGAGAGTTCACGCATCGAGCGAAGTCAGTTTCTATGGCTAAATTTACTGCACAGGAAGTTAGTGCCCTTCAAGAAGGAGGAAATGAG
upper sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G341732_T02 (Zea mays), 3'ss of exon 4
------------------------------------------------------------cattttgtttaa-aaaatattgga-gatagaataatatcatttctttctagtgttcacttttccttgaatgaaagtcaactgcttt-------ttgttttgattta-tagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
|||||||||| | |||| | | ||| || | | || ||| | | || | | ||| |||| | | | | |||| ||| ||||||||| ||||| |||||||||||||| ||||| ||||| || |||||| |||||||||||| ||| ||||||||||| || ||| ||
gtaagtattttagtgtgccctcttttagtttagacgaccaatctatcgagccttcccttcttttttgtttaacagtatatggcatgatggagtga-attattgggcac-accagtcccctggtgaaatatgccagtctttttcctaatataaatcactttgttttcctagTCGGGAGTTCACGCATCGAGTAAAATCGGTTTCCATGGCCAAATTTACTGCACAAGAAGTTACTGCCCTTCAAGAAGGGGGGAATGAG
upper sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G136547_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------cattttgtttaaaaaata---ttggagatagaataatatcatttctttctagtgttca-cttttccttgaatgaaagtcaactgcttt-ttgttttgatttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
| |||||| | || ||| | ||| | || | | | | | | | | | || || | | | | || |||| |||| || || || |||| |||||| ||||||||||| ||||||||||| || ||||| ||||||||| ||||||| |||||| |||||| ||
gtaagtggtgatcatattgttgtttttctctttattaaaagtgcagcaatgtttcttgtttggctattacagttgtgaactcctccctataagttatataaacttctgaaccagtgcctg--tgcttgcccatttctgaattgtgacattttacagCCGAGAGTTCAGTCATCGTGTAAAATCAGTATCAATGGCTAAATTCACTTCCCAAGAAGTTTCGGCACTTCTAGAAGGGGGCAATGAG
upper sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------cattttgtttaaaaaatattgga-gatagaataatatcatttctttctagtgttcacttttcctt--gaatgaaagtcaactgctttttgttttga-----------tttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
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gtaagtattttagggagccctcttttactttagtcaacctatttatcgagcttcactttctttttgtttaacaatatatcaatat-atgccttgatggaatgaactgtccccaagggaaatacgttggttttttcctaatatagatcactttatttttctagTCGGGAGTTTACACATCGAGTAAAATCTGTTTCCATGGCCAAATTTACCGCACAAGAAGTTGCTGCCCTTCAAGAAGGGGGGAATGAG
upper sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G126079_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------cattttgtttaaaaaatattggagatagaataatatcatttctttctagtgttcacttttccttgaatgaaagt--caactgctttttg--ttttga---tttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
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gtaagtggtgatcatattgttgtttttctctttattaaaagtgcagcaatatttcttgtttggc---tattacagttgtgaactcctccctacaagtta-tataaacttctgaaccagtgcctgtgcttgcccatttctgaatcgtgacattttacagCCGAGAGTTCAGTCATCGTGTAAAATCAGTATCGATGGCTAAATTCACTTCCCAAGAAGTTTCGGCACTTCAGGAAGGGGGCAATGAGMapped 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|209722104|gb|BW659319.1|BW659319EST: GTGTGCACAAACTTCTGGACGTTTGTTTGCACAAACTGCAGTGGAATACA TCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTC
genomic: GTGTGCACAAACTTCTGGACGTTTGTTTGCACAAACTGCAGTGGAATACAgtaagtcctt ... tgatttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagtgttcacttttccttgaatgaaagtcaactgctttttgttttgatttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
ttttgat putative branch site (score: 4)
ctgctttttgtttt CT-rich tract
tttttgttttgattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattttgtttaaaaaatattggagatagaataatatcatttctttctagtgttcacttttccttgaatgaaagtcaactgctttttgttttgatttatagTCGGGAATTCACTCATCGAGTAAAATCAGTTTCAATGGCTAAGTTTACTTCACAAGAAGTTAGTGCACTTCAAGAAGGAGGCAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactgc