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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA

Basic information

species Zea mays
transcript GRMZM2G403493_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G403493_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os07g07080.1 (Oryza sativa), 3'ss of exon 8
gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttg----ttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA
||||| ||| |||  || | ||||  ||||  ||| |||   ||| ||    |||||  || |||  ||   | | | |||||||||| || ||||||||||||||| ||||||||||||| |||||||| |||||||| ||  |||||||   |  |||||||||||| |||||||||||||
gtttg-tttgttaattgttgaggtactaatctgtacagc--caatctgtagtttcatacttacatt-caaagtgtttctacagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA

upper sequence: GRMZM2G403493_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 6
----------------------------------gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA
                                  ||||  | | || || |  |         ||| | ||  | || ||    |   ||||  | |  |  | | || |||| ||| | | ||||| ||||||||||| |||| ||| || ||||||||||||||||| || |  | ||||   || |||||||||| |||||||||||  |
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgat-taaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA

upper sequence: GRMZM2G403493_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA16G04300.1 (Glycine max), 3'ss of exon 6
------------------------------------gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA
                                     |||  ||| |  |  |  ||    |   ||| | ||  |  | ||    | | ||||  ||   |  | | |  |||| | | | | ||||||||||||||||| |||| ||| || ||||||||||||||||| || |  | ||||   || |||||||||| |||||||||||  |
gttcttattatgctctgaatttttctcttcacatgtattttatttttcccgagacaaaacat--gttgat-taaaaacacttcccccctttttgttta---tttttttttaacagTTGTATGCTATGTGTGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA

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: 47 (upstream exon), 49 (downstream exon)
Score: 236

AGTGATTTCAGTGGCTGGAACAACGCACAGTACTGCTTTAATAGCTGATGGTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 128

AGTGATTTCAGTGGCTGGAACAACGCACAGTACTGCTTTAATAGCTGATGGTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 162

AGTGATTTCAGTGGCTGGAACAACGCACAGTACTGCTTTAATAGCTGATGGTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 553

AGTGATTTCAGTGGCTGGAACAACGCACAGTACTGCTTTAATAGCTGATGGTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATTAACTGGTGATGTTTTCATGTGGGATGCAA
                                 gcataac  putative branch site (score: 553)
                                         tcatctct  CT-rich tract
                 taatttgtt  TA-rich tract