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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG

Basic information

species Zea mays
transcript GRMZM2G395549_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctga---ttcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
              |    | | ||   |||| || |||  | | |     | ||||   |   |  ||||| | |||    | |  ||  | |||| ||||||||||||||||||||||||||||||||| ||||||||| ||||||| ||||||||||||||  |||||| ||| |||||||||||||||||   |||||                                                                       
--------------gtttgtttcttatggcagggc-cttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG-----------------------------------------------------------------------

upper sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctga---ttcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
              |    | | ||   |||| || |||  | | |     | ||||   | | |  ||||| | |||    | |  ||  |||||| ||||||||||||||||||||||||||||||||| ||||||||| ||||||| ||||||||||||||  |||||| | | |||||||||||||||||   |||||                                                                       
--------------gtttgtttcttatggcagggc-cttctattggtctatcagttttgctccgtttcaaaattttgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG-----------------------------------------------------------------------

upper sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
gtaag--catctg-attgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
||| |  |||  |   | ||||| || ||    | |     |||         | ||    || ||       |||  | | | ||  |   ||    | ||||||||||  | | ||||||||||||||||||||||||| |||| || ||||| || |||||  | |||| ||| ||||||||| | |||||    ||||                                                                       
gtaggatcattagtggtaaaaatttaattagatattagttgttg---------catgccataactctaatgggaaacttcact-ttaatatgct----atagGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG-----------------------------------------------------------------------

upper sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
---gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
   | |   ||    |  | ||| |  |  |    |  |||||    | || |  | || || |||   | |  ||| |  | | |||      ||  | ||||||||||  | | |||||| || ||||| ||||||||| |||||||||||||||| |||||  | |||| |||| | |||||  | |||||    ||||                                                                       
gtagcattaatactgtcaacaatttcatcttaatttttacttt----ataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG-----------------------------------------------------------------------

upper sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgat-tcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
            | | |    ||||     |     | ||  |||  ||   |||| ||   | |  ||  |||  ||  | |  ||| | |    | ||||||||||  | | |||||||||||| |||||| ||||| |||| || |||||||| |||||  | |||| ||| ||||||||| | ||||||   ||||                                                                       
-----------gtaggatgaatattggcaaaaatttcattagatatcagt--tgttgcatgccataacactaatgggaaatttcattgatatgct-atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG-----------------------------------------------------------------------

upper sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
|| || | |||| |||  |  |  || |         |||  ||| || |       | |     |  || ||| || ||  |  || |||     ||||||||||| |||| |||| | || ||||| ||| ||||| ||||||| ||||||||||||||  | ||||  ||  |||||||| | || ||   ||| |                                                                       
gttagaagctgactgatgactttgtttt---------tttctataaaaacaactgagctacattacttaacaat-tggtttcttctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG-----------------------------------------------------------------------

upper sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
gtaagcatctgattgaaaatcta----tttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
|| ||   ||||      || ||    ||||||      ||||  |  |  ||     |  ||||   |  |  |    |  |||||||| ||  |    ||||||||||| ||||  ||| | || ||||||||||||||| ||||||| || ||||| |||||  | |||| |||  |||||||| | ||||    ||| |                                                                       
gttagaggctgaccattgatttaatattttctgttaaaaactt--atcaccagtggcttaacaatctatatctgatgattatttcttgtttctgatct--cagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG-----------------------------------------------------------------------

upper sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
--gtaagcatctgattgaaaatctatttctgcagtgcacttt---gaatagaagccctgtttcaat--tcctcccaaaaatctg---attctt----------gttgctctttgga---caggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
   |  |  | || | |    | | ||||     | |   ||    | ||     | ||||||  |    || | | |  | |    | ||||          |||  |  |||||   ||||| |||||  | ||||||||||| ||||||||||||||| |||||||||||||||| |||||  ||||||  || ||||||| | |||||||    ||||                                                                       
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG-----------------------------------------------------------------------

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 2 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 17 (downstream exon)
Score: 32

TCAGTTTTATTTGCAAGAGCATCCTGATCTCATCAATGATATGCTAAACGTGCTTGCACTTCGTTTAGATCACACCAGAGTTGTAGACATAATGCGCAAGgtaagcatct ... tgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG


Block sizes: 49 (upstream exon), 17 (downstream exon)
Score: 23

TCAGTTTTATTTGCAAGAGCATCCTGATCTCATCAATGATATGCTAAACGTGCTTGCACTTCGTTTAGATCACACCAGAGTTGTAGACATAATGCGCAAGgtaagcatct ... tgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
 gagtaac  putative branch site (score: 23)
                                         tttatgt  TA-rich tract