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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgcgattagtcggacgacttgaaatcattgtttgtgtctatattattatcccactattttggtattgtatttcatgttcaattttgttttacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGATCTGTCGTGAGTATGATTGACAGGATTGCTGGATCAGCGCCTGGTAATG

Basic information

species Zea mays
transcript GRMZM5G833477_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833477_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g45080.1 (Oryza sativa), 3'ss of exon 6
-tcgcgattagtcggacgacttgaaatcattgtttgtgtctatattattatcccactattttggtattgtatttcatgttcaattttgttttacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGATCTGTCGTGAGTATGATTGACAGGATTGCTGGATCAGCGCCTGGTAATG
     |  ||  |   |   ||  | | |   |  |  | ||  ||  | ||||  | ||||  |    |  ||||||| |  || |||| |  |   |||||| | |||||||| |   ||||| | ||||||||||| ||||| || || ||||| || || |||||||||||||||||||| || |||||||||||||
agaaggcatataccctccctttagattgaaattgaggatttaccttcctgtccctttttttttcttgcatgattcatgtccc-ttgtgttctgtatggcagTTGCGGACAACACAACGCCAGTCCTTGAGTGCTGCAGTAAGCGACATAGGTTCTGTTGTCAGCATGATTGACAGGATTGCTGGGTCTGCGCCTGGTAATG
















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|61118256|gb|DN559217.1|DN559217
EST:     CAACAAAATCAAGCGCAGCAGAAAGGCCTCTCGATCGCTTGCTTAAAGCA                         TTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGA
genomic: CAACAAAATCAAGCGCAGCAGAAAGGCCTCTCGATCGCTTGCTTAAAGCAgtaagtaact ... tacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGA
EST: gi|47961803|gb|CN844512.1|CN844512
EST:     CANCAAAATCAAGCGCAGCAGAAAGGCCTCTCGATCGCTTGCTTAA-GCA                         TTGAGAACAACACAGCCTGGGTCCCCTTAGTGCTGCAGTT
genomic: CAACAAAATCAAGCGCAGCAGAAAGGCCTCTCGATCGCTTGCTTAAAGCAgtaagtaact ... tacaatacagTTGAGAACAACACAGCCTGAGTCCC-TTAGTGCTGCAGTT

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), 41 (downstream exon)
Score: 62

AGAATTCACAAGTGCTGATGGAGGTCAGGTTAGCGTACCAACTCAAGTTCCAACAAAATCAAGCGCAGCAGAAAGGCCTCTCGATCGCTTGCTTAAAGCAgtaagtaact ... tacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGATCTGTCGTGAGTATGATTGACAGGATTGCTGGATCAGCGCCTGGTAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 35

AGAATTCACAAGTGCTGATGGAGGTCAGGTTAGCGTACCAACTCAAGTTCCAACAAAATCAAGCGCAGCAGAAAGGCCTCTCGATCGCTTGCTTAAAGCAgtaagtaact ... tacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGATCTGTCGTGAGTATGATTGACAGGATTGCTGGATCAGCGCCTGGTAATG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 90

AGAATTCACAAGTGCTGATGGAGGTCAGGTTAGCGTACCAACTCAAGTTCCAACAAAATCAAGCGCAGCAGAAAGGCCTCTCGATCGCTTGCTTAAAGCAgtaagtaact ... tacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGATCTGTCGTGAGTATGATTGACAGGATTGCTGGATCAGCGCCTGGTAATG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 83

AGAATTCACAAGTGCTGATGGAGGTCAGGTTAGCGTACCAACTCAAGTTCCAACAAAATCAAGCGCAGCAGAAAGGCCTCTCGATCGCTTGCTTAAAGCAgtaagtaact ... tacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGATCTGTCGTGAGTATGATTGACAGGATTGCTGGATCAGCGCCTGGTAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatcccactattttggtattgtatttcatgttcaattttgttttacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGATCTGTCGTGAGTATGATTGACAGGATTGCTGGATCAGCGCCTGGTAATG
                                     ttttgtttt  CT-rich tract
                                   aattttgttttacaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgcgattagtcggacgacttgaaatcattgtttgtgtctatattattatcccactattttggtattgtatttcatgttcaattttgttttacaatacagTTGAGAACAACACAGCCTGAGTCCCTTAGTGCTGCAGTTAGCGATATTGGATCTGTCGTGAGTATGATTGACAGGATTGCTGGATCAGCGCCTGGTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA