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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGACCGCTCTCGGTGGTTGAGTACAGCGAAATGGATGCGGCTATGGCTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttctatccttcgcttctcgttctctttcgccctccctccatccaaaaactgttctctccttttttttttttttgtag

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 11
TGGTGGACCGCTCTCGGTGGTTGAGTACAGCGAAATGGATGCGGCTATGGCTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttctatccttcgcttctcgttctctttcgccctccctccatccaaaaactgtt-----ctctccttttttttttttttgtag
||||||||| ||||| || |||||||| || |||||||| || ||||||||||| ||||| |||||||| || || || || ||||| ||||||||||| ||||| |||||||||| | |||||  || ||   |    | ||   ||   |      |     |      || || | |   || ||
TGGTGGACCTCTCTCTGTAGTTGAGTATAGTGAAATGGACGCAGCTATGGCTACTGAAATTAATCAGTCAACGGGACGCCTTCGTTATTGTTGGAGCAATgtatg-ttctatcctttgtttctcaatccctcctggttgcactttctcttgaggtgtataacaaccgcatgttcttatctcactgcag
















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|149100895|gb|EE186990.2|EE186990
EST:     AGGGCGACTCCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: AGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
EST: gi|211094109|gb|FL460556.1|FL460556
EST:     GACAGGGCGACTTCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: GACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
EST: gi|37378055|gb|CF625683.1|CF625683
EST:     CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
EST: gi|211406602|gb|FL094198.1|FL094198
EST:     CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
EST: gi|94477176|gb|EB706134.1|EB706134
EST:     AAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: AAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
EST: gi|37397991|gb|CF636304.1|CF636304
EST:     CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
EST: gi|91052248|gb|EB162666.1|EB162666
EST:     CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
EST: gi|24769018|gb|CA404147.1|CA404147
EST:     CTACCAAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
EST: gi|16926697|gb|BM079765.1|BM079765
EST:     CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAAC                         ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC
genomic: CTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGC

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: 44 (upstream exon), 48 (downstream exon)
Score: 53

TGGTGGACCGCTCTCGGTGGTTGAGTACAGCGAAATGGATGCGGCTATGGCTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 118

TGGTGGACCGCTCTCGGTGGTTGAGTACAGCGAAATGGATGCGGCTATGGCTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 146

TGGTGGACCGCTCTCGGTGGTTGAGTACAGCGAAATGGATGCGGCTATGGCTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

TGGTGGACCGCTCTCGGTGGTTGAGTACAGCGAAATGGATGCGGCTATGGCTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttct ... ttttttgtagATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGACCGCTCTCGGTGGTTGAGTACAGCGAAATGGATGCGGCTATGGCTACCGAAATGAATCAGTCGACAGGGCGACTCCGTTACTGTTGGAGCAACgtatggttctatccttcgcttctcgttctctttcgccctccctccatccaaaaactgttctctccttttttttttttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA