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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaactattttgcattttcatttcagtgaaaaaattctcatgctgtgagaaaaggtaatcaaaggttcttgcttatcactgttattatgactcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT

Basic information

species Zea mays
transcript GRMZM2G095611_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095611_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g63870.1 (Oryza sativa), 3'ss of exon 6
gtaagaaaactattttgcattttcatttcagt-gaaaaaattctcatgctgtga--gaaaaggtaatcaaaggttcttgcttatcactgttattatgactcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT
||||| ||    ||   | |||||   |  || | || | |   |||  | | |  |  |  | | |||  |||||||||| || ||  || || || | |  ||||||||||||| ||||| |||||||||||||||||||||||| | ||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| ||||||||
gtaagcaactatttgcactttttcccctgtgttggaagagtagacatcatttaactgtgacagcattca--ggttcttgct-ataacaattcttgtgtccccattgtagGAAAAGTTGGTGCCTTCATTGCTTCTATTCCTGATGTTCTAGTTGCTGCTCTTCTTTGTTTCATGTGGGCCATGCTATGTGCCCTTGGCTTATCCAATCT

upper sequence: GRMZM2G095611_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G09060.1 (Glycine max), 3'ss of exon 8
gtaagaaaactattttgcattttcatttcagtgaaaaaattctcatg-ctgtgagaaaaggtaatcaaaggttcttgcttatcactgttattatgactcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT
         || | |    ||  ||||| |   |       ||| || |||| | |||       ||||  |       | | | | |  ||||| |  |     ||| || || || | |||||||||||| ||||| || || |||||||||| |||||| ||||| |||||||| ||||||   ||  | |||||||| |||||
-----tcggct-tctcttgttcccatttgatatagttttgcctcttgtctgtaaaaaactccttgcaaatttatccatgtttaattttgcttatg-ccatacaacagGTAAGGTTGGAGGATTCATTGCTTCAATTCCCGAAGTCATGGTTGCTGGTCTCCTCTGCTTTATGTGGGCAATGCTCACAGCATTAGGCTTGTCAAATCT

upper sequence: GRMZM2G095611_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G30670.1 (Glycine max), 3'ss of exon 8
-gtaagaaaactattttgcattttcatttcagtgaaaaaattctcatgctgtgagaaaaggtaatcaaaggttcttgcttatcactgttattatgactcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT
 ||    | | | |||  ||| |   | |     ||    | ||||  ||||   |      |  ||||          | | | | |  || |      |    ||| || || || |  ||||||||||| |||||||| || |||||||||| |||||| ||||| ||||||||||||||    ||  | ||||||||||||||
ggtttttagagtctttcccatgtctctgttgc--aatctgtactca-actgtagaatttttcatgcaaataaaaacatgtttaattttacttgta----ctggacagGTAAGGTTGGAGGGTTCATTGCTTCAATTCCTGAAGTCATGGTTGCTGGTCTCCTATGCTTTATGTGGGCTATGCTTGCAGCATTGGGCTTGTCCAATCT

upper sequence: GRMZM2G095611_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G19420.1 (Glycine max), 3'ss of exon 8
gtaagaaaactattttgcattttcatttcagtgaaaaaattctcatg-ctgtgagaaaaggtaatcaaaggttcttgcttatc-actgttattatgactcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT
       | || | |    ||  ||||| |   |      ||||  | |||| | ||       |   |  ||  | | | |  | | ||  |    |  |     ||| || || || | |||||||||||| |||||  | || |||||||||| |||||| ||||| |||||||| ||||||   ||  | || ||||| |||||
-------agct-tctcttgttcccatttgatatagttttgtctctcgtctgtaaaaagctcctcttgtaaatttatccgtgtttaattttgcttatgccatacaacagGTAAGGTTGGAGGATTCATTGCTTCAATTCCCAAAGTCATGGTTGCTGGTCTCCTCTGCTTTATGTGGGCAATGCTCACAGCATTAGGATTGTCTAATCT

upper sequence: GRMZM2G095611_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G05280.1 (Glycine max), 3'ss of exon 8
---gtaagaaaactattttgcattttcatttcagtgaaaaaattctcatgctgtgagaaaaggtaatcaaaggttcttgcttatcactgttattatgactcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT
    |    |  || | |    | |  ||| || |    |        |    |     | |  ||| |||   | ||   | | |||  || |  |||        ||| || || || |  ||||||||||| ||||| || || |||||||||| |||||| ||||| |||||||| |||||    ||  | |||||||| |||||
ggtttttagagtctttctcatgtctctattgcaatttgtactcaactgtagaatttttcatgcaaataaaaacatgtttaattttacttgtactg-gac--------agGTAAGGTTGGAGGGTTCATTGCTTCAATTCCCGAAGTAATGGTTGCTGGTCTCCTATGCTTTATGTGGGCAATGCTTGCAGCATTGGGCTTGTCTAATCT

upper sequence: GRMZM2G095611_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv06s0061g01310.t01 (Vitis vinifera), 3'ss of exon 8
gtaagaaaactattttgcattttcatttcagtgaaaaaattctca-tgctgtgagaaaaggtaatcaaaggttcttgcttatc-actgttattatgactct-tttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT
         |  ||       |||||    ||    |  |    | | || ||  |     ||||  |  |  |||      | | | | |||   |   | ||   ||| ||||| || |  || |||||||| |||||||| || ||||||||||||||||| |||||||||||||| |||||    ||  | || ||||| ||| |
---------cctttcattgacttcataaaggtatggaggtctctacttctctgctatcctttaatttattgcccttcaaggcctaatctcatttcaatcatgttcacagGTAAAGTTGGAGGGTTTATTGCTTCAATTCCTGAAGTCATGGTTGCTGCTCTCCTGTGCTTCATGTGGGCAATGCTTGCAGCATTGGGGTTGTCAAATTT

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 4 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 29

ACAATAACAGAGAATGTACACACAATTGCTGTGACTAAAATGGGTAGTCGACGAGCAGTTGGATTCGGTGCTATTTTACTTATACTGCTTTCTATTGTTGgtaagaaaac ... tcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT


Block sizes: 45 (upstream exon), 37 (downstream exon)
Score: 4

ACAATAACAGAGAATGTACACACAATTGCTGTGACTAAAATGGGTAGTCGACGAGCAGTTGGATTCGGTGCTATTTTACTTATACTGCTTTCTATTGTTGgtaagaaaac ... tcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 3

ACAATAACAGAGAATGTACACACAATTGCTGTGACTAAAATGGGTAGTCGACGAGCAGTTGGATTCGGTGCTATTTTACTTATACTGCTTTCTATTGTTGgtaagaaaac ... tcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 3

ACAATAACAGAGAATGTACACACAATTGCTGTGACTAAAATGGGTAGTCGACGAGCAGTTGGATTCGGTGCTATTTTACTTATACTGCTTTCTATTGTTGgtaagaaaac ... tcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaaaaggtaatcaaaggttcttgcttatcactgttattatgactcttttgtagGAAAAGTCGGTGCATTCATTGCTTCTATTCCTGATGTTATGGTTGCTGCTCTCCTTTGCTTCATGTGGGCTATGCTCTGTGCTCTTGGCTTGTCCAATCT
                                            ctcttttgt  CT-rich tract
                                 tgttattat  TA-rich tract