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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgtctagtttgcctctgccttctctccaaaatgccgtcgccagtcaggccttgagcgatagagtaggcaaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC

Basic information

species Zea mays
transcript GRMZM2G044629_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 12
gtgagtgttgtctagtttgcctctgccttctctccaaaatgccgtcgccagtcaggccttgagcgatagagtaggcaaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC
                             |||| |  ||    || |  || || |  |  | |   |   |     |     ||| ||| |  ||    |||      |  |     | |||||  ||| || ||||| ||||||||||||||||||||||||||||||| | | | |||| ||||||||||||||| |||||||||||| ||||  |||||||| |||
-----------------------------ctcttcctaagaaagt-gagagccatgtttaaaactgcaagctccatcattcattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC
















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:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|71429564|gb|DR810614.1|DR810614
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATCCCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|211094109|gb|FL460556.1|FL460556
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTCCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|37378055|gb|CF625683.1|CF625683
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACATTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|211406602|gb|FL094198.1|FL094198
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|78115802|gb|DV534190.1|DV534190
EST:     GGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: GGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|94477176|gb|EB706134.1|EB706134
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|37397991|gb|CF636304.1|CF636304
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|211119105|gb|FL479440.1|FL479440
EST:     ACTYTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGMCAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|91052248|gb|EB162666.1|EB162666
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|24769018|gb|CA404147.1|CA404147
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|71772484|gb|DR970416.1|DR970416
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
EST: gi|16926697|gb|BM079765.1|BM079765
EST:     ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGT                         ATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG
genomic: ACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGG

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), 48 (downstream exon)
Score: 119

ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 237

ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 360

ATCTGCCTGCACATGTTCACTCTGGACTTCTTGAACCAAGTGGCAAACAGCCTTGAGAAGGACAGTGTgtgagtgttg ... ttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC
                    gcctgac  putative branch site (score: 360)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgttgtctagtttgcctctgccttctctccaaaatgccgtcgccagtcaggccttgagcgatagagtaggcaaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC