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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactattcttttcccttatggaatcccagctgtatgcataatgtgcgaacagacacagtttggtcattcgagacatctggtacatttttgtttgatgttattggactgatttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG

Basic information

species Zea mays
transcript GRMZM2G335287_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 12
gtgactattcttttcccttatggaatcccagctgt-atgcataatgt--gcgaacagacaca----------gtttggtcattcgaga-catctggtacatttttgtttgatgttattggactgattt-cgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG
|| |  | || |||   || | ||||| ||   || |||  ||||         || |  ||          |||| |  ||   ||| ||||| |    |     ||  || ||||  || | ||||   || ||||||| |||||||||| ||||| ||| | ||||||||||||||  ||||||| || ||||| ||||| |||||||| ||||| ||||||||||||| |
gt-atgactcatttgatttgtagaatctcaaaagtgatgtttaatcctatttgtcatattcattttctatttgttttgctatcttagatcatcttggtgctgcacattatatattatgtgatttatttgtcaaccagGATGCTGGAGAAAGTCTGCAAGGATTCACAAATGCTTGCAGACATGTTTGTAAATTATGATTGTGACCTTGAGGGGCCAAACCTTTTTGAACGCATG

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 15
gtg-actattcttttccctta--tggaatcccagctgtatgcataatgtgcgaacagacacagtttggtcattcgagacatctggtacatttttgtttgatgttattggactgatttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG
||  | | |||||     ||   |  |||      ||  |  | | | ||  ||   |     ||  ||  || |  |   ||  | ||| || |||   |    || |  ||  || |   ||||||||| |||||||| || || ||||| || |||||||  ||  | |||||||| ||||| ||||||||||||| ||||||  | |||||||| | |
gtataatgttcttcctggttgattaaaatattgcttgattataaactttgttaatgaaatttcttgtgttgtttgccattccttttccatatt-gttaatttggtttagtgtgggtttg---cagGATGTTAGAGAAAGTATGTAAGGATCCACAGATGCTTGTTGACATCTTTGTGAATTATGATTGTGATCTTGAGGCACCAAACTTGTTTGAACGAATG

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 14
gtgactattcttttcccttatggaatcccagctgtatgcataatgtgcgaacagacacagtttggtcattcgagacatctggtacatttttgtt-tgatgttattgga--ctgat----ttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG
       | |  |    || ||     |||| ||||   ||  |||    | | |||    || | ||   |||   |||  ||  |||||| | |||  ||  ||||  || ||    ||| |  ||||||| | |||||||| ||||||||||| || |||||||  ||||||| ||| |||||||| |||||||| ||||  |||||  | ||||| |||| |
------gtacaatatttttctgctcgtccagatgta---attttgttttga-atacatctcttaggcaagtgag---tctattatctttttgctgtgaatttcatggatactcatatttttctacgcagGATGCTTGAGAAAGTCTGCAAAGATCCTCAGATGCTTGTTGATGTGTATGTAAACTATGATTGTGATCTAGAGGCCCCAAACTTGTTTGAGCGCATG

upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 15
gtgactattcttttcccttatggaatcccagctgtatgcataatgtgcgaacagacacagtttggtcattcgagacatctggtacatttttgtttgatgttattggactgatttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG
   || ||   ||       || |||    |   | |||| | |   | ||||     |  |||||  ||     | ||||  |  |  |  ||  |          ||||||| |   ||||||| | ||||||||||| ||||||||||| |||||||  ||  | | |||||||||||| |||||||||||||  |||||  | ||||| |||| |
--aacaatcaattagatccttgaaattaaggaattgtgcagattt--ctaacat---taacttggttcttt---tcctctgtgatctcctgattgaac---------ctgattttg---cagGATGCTTGAGAAAGTTTGTAAAGATCCCCAGATGCTTGTTGACATATATGTGAACTATGATTGTGATCTTGAGGCCCCAAACTTGTTTGAGCGCATG

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: 49 (upstream exon), 49 (downstream exon)
Score: 186

GGGGAAATTGGTGTCTTCTTTCCTCTGATAGTTTTAAGGTCTTTGGATAGCTCTGATAGCTCCCTCAGCCAGAAGGCTAGTGTTCTTAGgtgactattc ... ttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 113

GGGGAAATTGGTGTCTTCTTTCCTCTGATAGTTTTAAGGTCTTTGGATAGCTCTGATAGCTCCCTCAGCCAGAAGGCTAGTGTTCTTAGgtgactattc ... ttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

GGGGAAATTGGTGTCTTCTTTCCTCTGATAGTTTTAAGGTCTTTGGATAGCTCTGATAGCTCCCTCAGCCAGAAGGCTAGTGTTCTTAGgtgactattc ... ttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GGGGAAATTGGTGTCTTCTTTCCTCTGATAGTTTTAAGGTCTTTGGATAGCTCTGATAGCTCCCTCAGCCAGAAGGCTAGTGTTCTTAGgtgactattc ... ttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgagacatctggtacatttttgtttgatgttattggactgatttcgaatcagGATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACG
                                      gactgat  putative branch site (score: 190)
                  atttttgttt  TA-rich tract