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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggttgttccatttgccatttctactatatgtagtatcagcagcatatttgcaatgtcgagatgtgcaattttgttttttttcgtggtgcccatgtactcctgctgacactaaaattatcttgtcagTTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTCTTTATTGCATGTCATTGGTCTTTGTTGTTGCATTTAACCACTATCTCTA

Basic information

species Zea mays
transcript GRMZM2G144254_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 6
gtatgggttgttccatttgccatttctactatatgtagtatcagcagcatatttgcaatgtcgagatgtgcaattttgttttttttcgtggtgcccatgtactcctgctgacactaaaattatcttgtcagTTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTCTTTATTGCATGTCATTGGTCTTTGTTGTTGCATTTAACCACTATCTCTA
                              | ||| ||     | || || |||  |||||   |   |   |  || | || | ||  | | ||   ||     | ||||  | | ||| || |   |||||||||| |||||||||||  | || |||||||||||||| ||||||||||| |||||||||||| |||||||||| |||||||| || || ||||||||
----------------------------aaaaatggagggaggg-agtat-tttataatgtactgcaattttacgttatcttatctca-gttccctgagtgaatattctgatgccataatcatttcaacagTTTACACCCCGGAGCAGCTAGTTGCGAAATACAGCAATTTAGTGTTTGTTCTCTATTGCATGTCACTGGTCTTTGTGGTTGCATTCAATCAGTATCTCTA
















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|78022546|gb|DV490933.1|DV490933
EST:     AGTCTTTGGCAACATCTTCTTAGTATCCTTTGGCAACCATCAATCACCTG                         TTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTC
genomic: AGTCTTTGGCAACATCTTCTTAGTATCCTTTGGCAACCATCAATCACCTGgtatgggttg ... atcttgtcagTTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTC




















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: 48 (upstream exon), 48 (downstream exon)
Score: 83

AGTCATGGTAGCCACAACATTTATAGTCTTTGGCAACATCTTCTTAGTATCCTTTGGCAACCATCAATCACCTGgtatgggttg ... atcttgtcagTTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTCTTTATTGCATGTCATTGGTCTTTGTTGTTGCATTTAACCACTATCTCTA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 100

AGTCATGGTAGCCACAACATTTATAGTCTTTGGCAACATCTTCTTAGTATCCTTTGGCAACCATCAATCACCTGgtatgggttg ... atcttgtcagTTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTCTTTATTGCATGTCATTGGTCTTTGTTGTTGCATTTAACCACTATCTCTA


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 101

AGTCATGGTAGCCACAACATTTATAGTCTTTGGCAACATCTTCTTAGTATCCTTTGGCAACCATCAATCACCTGgtatgggttg ... atcttgtcagTTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTCTTTATTGCATGTCATTGGTCTTTGTTGTTGCATTTAACCACTATCTCTA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 61

AGTCATGGTAGCCACAACATTTATAGTCTTTGGCAACATCTTCTTAGTATCCTTTGGCAACCATCAATCACCTGgtatgggttg ... atcttgtcagTTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTCTTTATTGCATGTCATTGGTCTTTGTTGTTGCATTTAACCACTATCTCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttttttcgtggtgcccatgtactcctgctgacactaaaattatcttgtcagTTTACACGCCGGAGCAGCTGATAGCAAAATACAGCAATTTGGTGTTTGTTCTTTATTGCATGTCATTGGTCTTTGTTGTTGCATTTAACCACTATCTCTA
                                   cactaaa  putative branch site (score: 61)
                                           ttatctt  CT-rich tract
                                    actaaaattatctt  TA-rich tract