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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA

Basic information

species Zea mays
transcript GRMZM2G443668_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443668_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g07080.1 (Oryza sativa), 3'ss of exon 8
gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttg----ttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA
||||| ||| |||  || | ||||  ||||  ||| |||   ||| ||    |||||  || |||  ||   | | | |||||||||| || ||||||||||||||| ||||||||||||| |||||||| |||||||| ||  |||||||  ||  |||||||||||| |||||||||||||
gtttg-tttgttaattgttgaggtactaatctgtacagc--caatctgtagtttcatacttacatt-caaagtgtttctacagATATTCTCTATGTGTGGAAGGAATGTTGTGAACATCTCAGCTGGAAAATACTGGACTGCATTGGCTACCGCAGGTGGTGATGTTTTTATGTGGGATGCAA

upper sequence: GRMZM2G443668_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA19G29100.1 (Glycine max), 3'ss of exon 6
----------------------------------gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA
                                  ||||  | | || || |  |         ||| | ||  | || ||    |   ||||  | |  |  | | || |||| ||| | | ||||| ||||||||||| |||| ||| || ||||||||||||||||| || |  | |||| | || |||||||||| |||||||||||  |
gttcttattatcctctgaaattttctcttcacgtgttttttatttttcccgagacaaaacatgttgat-taaaaatacttccccccgttttgttttaatttttttttgaacagTTATATGCTATGTGCGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA

upper sequence: GRMZM2G443668_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA16G04300.1 (Glycine max), 3'ss of exon 6
------------------------------------gtttggtttcttacctgctaaggtcttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA
                                     |||  ||| |  |  |  ||    |   ||| | ||  |  | ||    | | ||||  ||   |  | | |  |||| | | | | ||||||||||||||||| |||| ||| || ||||||||||||||||| || |  | |||| | || |||||||||| |||||||||||  |
gttcttattatgctctgaatttttctcttcacatgtattttatttttcccgagacaaaacat--gttgat-taaaaacacttcccccctttttgttta---tttttttttaacagTTGTATGCTATGTGTGGAAGGAATATGGTGAGCATATCAGCTGGAAAGTACTGGACTGCAGCAGTTACAGCTACAGGTGATGTTTACATGTGGGATGGGA

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|31348863|gb|CD433220.1|CD433220
EST:     GTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAG                         ATATTTTCAATGTGTGGGAGGAATATCGTGAACATCTCGGCTGGAAAGTAC
genomic: GTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTAC




















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: 131

GATTTCAGTGGCTGCTGGAACAACGCACAATACTGCTTTAACAGCTGATGGTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

GATTTCAGTGGCTGCTGGAACAACGCACAATACTGCTTTAACAGCTGATGGTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 44

GATTTCAGTGGCTGCTGGAACAACGCACAATACTGCTTTAACAGCTGATGGTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

GATTTCAGTGGCTGCTGGAACAACGCACAATACTGCTTTAACAGCTGATGGTGCTCTTTTCTACTGGGTTTCATCAGATCCTGATCTAAAATGCCAGCAGgtttggtttc ... ctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattggtatagcagtaatttgttcatgtttgcataacatcatctctgtacagATATTTTCAATGTGTGGAAGGAATATTGTGAACATCTCGGCTGGAAAGTACTGGACCGCTGTGGCTACATCAACTGGTGATGTTTTCATGTGGGATGCAA
                                 gcataac  putative branch site (score: 177)
                                         tcatctct  CT-rich tract
                 taatttgtt  TA-rich tract