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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcctaataagataaactaagaagccatgcaaaatatttgcaatccagatgtattgttacattgcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgttgttgcttttccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG

Basic information

species Glycine max
transcript GLYMA01G41790.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g01650.2 (Oryza sativa), 3'ss of exon 5
gtaatcctaataagataaactaagaagccatgcaaaatatttgcaatccagatgtattgttacattgcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgttgttgcttttccatttcagGTTGGA---TCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG
                                        |||   |||   |  ||  ||    | | |   |||||   |  |||  | || | |   | ||| ||    |  ||| |   ||     ||||       ||| ||     || ||  | ||||| ||||||||| | |||||| ||||| | |||||||||||||| || ||||||||||| ||||||||||  |||||||   
---------------------------------------cttgacttcccattccatgattttcatacattt-tagttctcatcttttatcgtgtgtggatcattaggg---ttgaacctaacttagcatttttgttggatagGCTGTGAATTCTAAGAGCATGCTGGATGATTGGCAAGAGAATTTGGCTATTATAACTGCAAACAGGACGAAAGGTGATGATCTTGTAATTACGCACCTTG---

upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 5
gtaatcctaataagataaactaagaagccatgcaaaatatttgcaatccagatgtattgttacattgcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgtt-gttgcttttccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG
                                       |||||      |||      ||  | || |  |  |  |     |||  | | ||||| ||| | |  |  |||||   | |  ||  ||| |||  ||   |||  | |  | ||||| ||| | ||||| |||||||||||| ||||| | ||||||||||| || || |||||||| || || || ||||  || ||||| |
--------------------------------------ttttgcttcattgataatgcattctactgttctaccacctc----gttgttggctttctgtttaaat-agtggctcactttataattcattgttttgtcaca-cagCCTAGTCCTAATGGCATGTTGGATGACTGGGAGGAGAATTTGGCTATCATAACTGCAAATAGGACAAAAGGTGACGACCTAGTTATTACCCATCTTGGAG

upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G163277_T01 (Zea mays), 3'ss of exon 5
--------------------------gtaatcctaataagata--aactaagaagccat-gcaaaatatttgcaatccagatgtattgttacatt---gcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgttgttgcttttccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG
                           |  |  |  | | ||      | |  | | || ||| ||| | |    | | |  || |  | |  ||   |  ||| |       || |||  || |||    || | ||      |  |   ||||||     ||| |    ||||  |||  | ||||||||| | |||||||||||||||||| | ||| | || |||||||||||||| |||||||| || || ||||| |  || |||||||
gtacttgcaaagttaatggtttttaattgtttttgctgacattttgtttgattaacgattgcataatgtcttgtttactgcagtgtcatgatttttgggtatcacttaccaataattttcctgcttttctatttactttcttttttgataatttgtt-----tttcctgagtcagCCTGGTCCTAATGGTATGTTGGATGATTGGGAGGAGAATTTAGCTATTATTACTGCAAACAGAACGAAAGGTGACGATCTAGTAATCACCCATCTTGGTG

upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G442742_T01 (Zea mays), 3'ss of exon 1
gtaatcctaataagataaactaagaagccatgcaaaatatttgcaatccagatgtattgttacattgcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgttgttgcttttccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG---
                                ||| | | || |  ||||    |   ||     ||   ||| |   |  ||||  ||       |  |||| ||      |   | |||    |||  ||| |    ||||  |||    |||   ||| | |||||||||||||||||| ||||| | || |||||||||||||| |||||||| |  || ||||| |  || |||||||   
------------------------------aacaataaacttcc--tccaataattgggtc---ctgaaacaagaagcttgaagtc-atgatgacatgattgactttt---tttgcaattt----gtttttttcctgagtcagCCTGGTCGTAAT---ATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAAAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT

upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G104958_T02 (Zea mays), 3'ss of exon 6
gtaatcctaataagataaactaagaagccatgcaaaatatttgcaatccagatgtattgttacattgcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgttgtt-gcttttccattt---cagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG
                                           ||    || ||    ||  ||||   | |  ||    |||  || || |   |  | | | ||     ||  ||  ||||    | | || |   |||   |||| ||   | || |||||||| ||||| ||| | |||||| ||||| | ||||| |||||||| || ||||||||||| ||||||||||  | |||||| |
-------------------------------------------caggagagctgc---gtatcattatattagaaggag-aaatcttgttagacacgctcttactttttcactgtaatatttgaaactcgtttctgggtttgtgcagGCTGCTCCTAAAGGTATGCTGGATGACTGGCAAGAGAATTTGGCTATTATAACAGCAAACAGGACAAAAGGTGATGACCTTGTAATTACCCGCCTTGGGG

upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G429241_T01 (Zea mays), 3'ss of exon 5
gtaatcctaataagataaactaagaagccatgcaaaatatttgcaa--tccagatgtattgttacattgcttcaatagttt-caaagtttattggtttctatttgatttggaagctcaaacttttgttgttgcttttccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG---
                                         ||||   ||  ||  | | | ||       |||||| ||| |  ||||| ||   ||   | ||| ||       |||   |||||| ||  ||| |    ||||  |||  | |||   ||| | |||||||||||||||||| ||||| | || ||||||||||||||  ||||||| |  || ||||| |  || |||||||   
-----------------------------------------tgcagcttcatgacttttgggtatcacttatcaataattttcctagttttttttgtttactctgacttttttttgcaa---tttgttttt--tttcctgagtcagCCTGGTCCTAAT---ATGTTGGATGATTGGGAGGAGAATTTGGCTATTATTACTGCAAACAGAACAGAAGGTGACGTTCTAGTAATCACCCATCTTGGTGATT

upper sequence: GLYMA01G41790.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv00s0229g00030.t01 (Vitis vinifera), 3'ss of exon 5
gtaatcctaataagataaactaagaagccatgcaaaatatttgcaatccagatgtattgttacattgcttcaatagtttcaaagtttattggtttctatttgatttggaagctcaaacttttgttgttgcttttccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG
                            |   |  || ||||   |      | ||||||  | |||| |||| |   ||    | | |  || ||| |            ||||| ||||| || |    ||||||     | ||||  | ||| ||||||| || |||||||| |||||| ||||||| |||||||| || ||||| |||| ||||||||||||| ||||||| ||||| |
--------------------------ttcgaccttaacattttgcaaaagtttctattgtatctttgcctcaacaagctctctctctctgtgtctctct------------ctcaatcttttcttatgaaatttcca-----gTTTGGGGCTAATAGTATGCTAGACGATTGGGAAGAGAATTTGGCTGTGATAACTGCCAATAGAACAAAAGATGATGAACTTGTACTTATTCATCTTGGAG

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|21888423|gb|BQ741636.1|BQ741636
EST:     CAAATAGTGGGCATCCTGGTGCTTCTGATATGTCTCAGCAGTCTCCACAG                         GTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATA
genomic: CAAATAGTGGGCATCCTGGTGCTTCTGATATGTCTCAGCAGTCTCCACAGgtaatcctaa ... tccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttctatttgatttggaagctcaaacttttgttgttgcttttccatttcagGTTGGATCCAATGGTATGCTTGATGATTGGGAGGAGAATCTGGCTGTAATAACTGCAAACAGAACCAAAGGTGATGAACTTGTAATTATTCACCTTGGTG
         atttgat  putative branch site (score: 5)
                                      ttgcttttccatttc  putative PPT
        tatttgattt  TA-rich tract