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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctcaaatgaacacacatattatctgtgtggtatttcgaggtagtatatacataggttgactaatctctttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG

Basic information

species Zea mays
transcript GRMZM2G420865_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 3'ss of exon 3
gtatctcaaatgaacacacatattatctgtgtggtatttcgaggtagtatatacat--aggttgactaatctctttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
|||| |  ||| |||| | |  |    |  |  | |||| ||   ||||| ||  |  || || | | | |||||||   ||||||||||||||||| || |||||| |||||||||||||||| || || || |||||||||||||||||||||||||| ||||||||||| ||||||||||
gtatatataattaacaaaaacttccctttgggagcattttgaatcagtatctatctttagcttaattgaactcttta---tagACAGCTGCTTTCTCATTACCTGTGCTGGAACGTCTACTTTTCCGGCCCAAACGTGTACCTGCAATTAGGGTGCTTATCCTTACTCCAACAAGAGAGTTGG

upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G25240.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------gtatctcaaatgaacacacatattatctgtgtggtatttcgaggtagtatatacataggttgactaatctctttaagt-tagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
                                                          || |      |||       ||| ||  ||||  | |||  |     | | | ||||   || ||| | | |||   |  |||||||||| ||  |  | |||   || ||  |  |  | || |||||||||||  | | |||||| ||||| || ||||||||||| |||||||||||||
gtaatctctttgttactttctttgggtgtttgttaatttgtgatgccttgcttctgtggtttggtgcctgagtttctgtatgatg-gtgtt-tcttttaatcccctttgttcatatcctg-ctattgtgtttccatgcagACAGCTGCATTTGCACTACCTACTTTAGAGAGGTTGTTGTTCCGTCCAAAGCGCATGCGTGCAATAAGGGTCCTCATTCTTACTCCGACCAGAGAGTTGG

upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G11950.1 (Glycine max), 3'ss of exon 3
-------------gtatctca-aatgaaca-----cacatattatctgtgtggta-tttcgaggtagtatatacataggttgactaatctctttaagt-tagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
             || |||   ||||  |      || || ||     |||| |  |||  | |   | | | ||||  ||| ||| | | |||   |  |||||||||| ||  |  | |||   || ||  |  |  | || |||||||||||  | | |||||| ||||| || |||||||||||||||||||||||| 
atcttgctattgtgtttcttttaatgccctttgttcatatcttgctattgtgtttcttttaatgccctttgttcatatcttg-ctattgtgtttccatgcaGACAGCTGCATTTGCACTACCTACTTTAGAGAGGTTGTTGTTCCGTCCAAAGCGCATGCGTGCAATAAGGGTCCTCATTCTTACTCCAACCAGAGAGTTG-

upper sequence: GRMZM2G420865_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g14540.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------gtatctcaaatgaacacacatattatctg-----tgtggtatttcgaggtagtatatacata--ggttgactaat-ctctttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
                                                                  | |  | ||||  ||  |  |  | |||     |    || ||   |||  | |  | |||  | ||    | | ||| || |   |||| ||||| || || || |||   || ||  |  || | || |||||||| ||||| |  ||||| ||||| ||| ||||||||||||||||||||||||
gtatgttgtgcgtcttgggtgcttgtgtaattgactctataatgtactactatgaaaacgagttgattttactaatgggcaagctgaaaaactgaaaccttctctagttatcggttctgtgaaaataatgatttgggattgctcctttacacagACGGCTGCCTTTTCCTTACCTACATTAGAGAGGTTATTGTTCCGTCCAAAACGTGTGCAAGCAATCAGGGTCCTTGTTCTTACTCCAACCAGAGAGTTGG

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|67017959|gb|CO446708.1|CO446708
EST:     CATTAACTGGAAGGGACATCTGTGGTAGTGCTATTACAGGATCTGGAAAG                         ACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAG
genomic: CATTAACTGGAAGGGACATCTGTGGTAGTGCTATTACAGGATCTGGAAAGgtatctcaaa ... tttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAG




















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), 47 (downstream exon)
Score: 277

GCTGCTTGCATTCCTCTGGCATTAACTGGAAGGGACATCTGTGGTAGTGCTATTACAGGATCTGGAAAGgtatctcaaa ... tttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

GCTGCTTGCATTCCTCTGGCATTAACTGGAAGGGACATCTGTGGTAGTGCTATTACAGGATCTGGAAAGgtatctcaaa ... tttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GCTGCTTGCATTCCTCTGGCATTAACTGGAAGGGACATCTGTGGTAGTGCTATTACAGGATCTGGAAAGgtatctcaaa ... tttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 141

GCTGCTTGCATTCCTCTGGCATTAACTGGAAGGGACATCTGTGGTAGTGCTATTACAGGATCTGGAAAGgtatctcaaa ... tttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgtggtatttcgaggtagtatatacataggttgactaatctctttaagttagACAGCTGCTTTCTCTTTGCCTGTGTTGGAACGTCTACTTTTTCGTCCAAAGCGTGTACCTGCAATTAGGGTGCTTATTCTTACTCCAACCAGAGAGTTGG
                                   gactaat  putative branch site (score: 141)
                                         tctcttt  CT-rich tract
                     tatatacata  TA-rich tract