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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttaatagtgttaactgttaatcagtatttctctcctacatggtataaaattgtttatattaatgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC

Basic information

species Glycine max
transcript GLYMA16G33380.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 6
--gtaacttaatagtgttaactgttaatcagtatttctctcctacatggtataaaattgtttatattaatgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC
| ||| || | || | | | | |||||| | | || | || | | | | | | | || | | | || | ||||||| |||||||| | ||||||||| | ||||| ||||||||||||||||||| | | | | | || |
gtattgcttgatcattgtatcagatggt-gttatttcctttgttgattttttagtctgttctgaaacatttagtg-------tctctcattttcagCATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACC

upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G069765_T03 (Zea mays), 3'ss of exon 6
gtaacttaatagtgttaactgttaatcagtatttctctcctacatggtataaa--attgtttatat--taa----tgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC----------------------------
|| || | | |||||| | | || | |||| | || ||||||| ||| |||| | | |||| | || | |||||||| ||||||| | || |||||||||||||| |||||||||||||||||| || | ||| | ||||
--------gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgtatttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCGTAAGTTTACAGTGAACATATATTTTGT

upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 6
gtaacttaatagtgttaactgttaatcagtatttctctcctacatggtataa--aattgtttata--ttaa----tgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC
|| || | | |||||| | | || | |||| | || |||||| |||| |||| | | |||| | || | |||||||| ||||||| | || |||||||||||||| |||||||||||||||||| || | ||| | ||||
--------gtaagattcctttattctcagtactgcactttactagggtaatacctgttttttatatcttaacttctgaaacttgtatttttcttatcttcagCATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATC

upper sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 6
-----gtaacttaat----agtgttaactgttaatcagtatttctctcctacatggtataaaattgtttatattaatgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC
| ||| || ||| | | ||| | || | || | | || || | || ||| || ||||| | || | ||||||| ||||||| | || |||||||||||||| |||||||||||||||||||| | ||| | ||||
gtaagattcctttattctcagtactg-cagtttactagggtaatacttgacttttattcttgatctcttgtcttctggaa--cttatattttctcatcttcagCATACACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGCCGGTTGATGTGAATGATC

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|16284063|gb|BI945885.1|BI945885
EST:     TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAG                         CATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA
genomic: TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAGgtaacttaat ... taatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA
EST: gi|12774002|gb|BG238929.1|BG238929
EST:     TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAG                         CATATGCCAAAGCTTTGGAGGATGCT-TTGCTGTTCTTGACAAAATTGCAA
genomic: TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAGgtaacttaat ... taatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA
EST: gi|16276828|gb|BI942066.1|BI942066
EST:     TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAG                         CATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA
genomic: TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAGgtaacttaat ... taatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA
EST: gi|16278542|gb|BI942959.1|BI942959
EST:     TGTCGCCGATGCATTCATTGACAAAATGCACCCTACAGTTATTTGCCGAG                         CATATGCCAAAGCCTGGGAGGATGCTATTGCTGTTCTTGACAGAATTGC
genomic: TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAGgtaacttaat ... taatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGC
EST: gi|24206236|gb|BU965489.1|BU965489
EST:     TGTCGCGGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAG                         CATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA
genomic: TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAGgtaacttaat ... taatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA
EST: gi|162286128|gb|FC456630.1|FC456630
EST:     TGTCGCGGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAG                         CATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA
genomic: TGTCGCCGATGCATTCATTGACAAAATTCACCCTACAGTTATTTGCCGAGgtaacttaat ... taatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacatggtataaaattgtttatattaatgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC
                      tattaat  putative branch site (score: 2)
 tataaaattgtttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttaatagtgttaactgttaatcagtatttctctcctacatggtataaaattgtttatattaatgaatgctacaattttgtaatatgcagCATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT