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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttattctatggatgctgattcattgcatgtataacttattattattgggatgtttttttgtgataattcaatggttgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTTCGTTGGCCTGCTGGAACCGATGGAGTTCTT

Basic information

species Zea mays
transcript GRMZM2G028796_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028796_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g41360.1 (Oryza sativa), 3'ss of exon 2
gttgttattctatggatgctgattcattgcatgtataacttattattattgggatgtttttttgtgataattcaatggttgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTTCGTTGGCCTGCTGGAACCGATGGAGTTCTT
||||| | ||  |||||||||| |  |   || |  ||  | | ||   | |   ||  |      |||  |  ||  ||    |||||||  | ||||||| | |||||||||| |||||  |||| ||||| ||| | || ||||||||||| || ||||||||||||
gttgtcactccttggatgctgaatactctgat-tgcaatgtctgatgtgttgctggtacta--acaatatattgattattctttttcagGCAGCCATTGCAGCAGCTGGTGGTATAAAGGCTTTGGTCGATCTCATACTCCGCTGGCCTGCTGGGACTGATGGAGTTCTT
















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|211104624|gb|FL034749.1|FL034749
EST:     AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
EST: gi|211104622|gb|FL034747.1|FL034747
EST:     AANAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTTTATTGCAGTATCTGGNGGTATCAAGGCCCTGGTAGATCCTAATATT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATC-TAATATT
EST: gi|211104625|gb|FL034750.1|FL034750
EST:     AAGAGGCTGCTGGTGGCCTNTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
EST: gi|211104626|gb|FL034751.1|FL034751
EST:     AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
EST: gi|211104621|gb|FL034746.1|FL034746
EST:     AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTCTATTGCAGTATCTGGTGGTATCAAGGNCCTGGTAGATCTAATATTT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
EST: gi|211104623|gb|FL034748.1|FL034748
EST:     AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
EST: gi|211102157|gb|FL034743.1|FL034743
EST:     AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTCTATTGCAGTATCTGGNGGTATCAAGGCCCTGGTAGATCTAATATTT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
EST: gi|211104620|gb|FL034745.1|FL034745
EST:     AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT
EST: gi|211104619|gb|FL034744.1|FL034744
EST:     AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAG                         GCGTCTATTGCAGTATCTGGTGGCATCAAGGCCCTGGTAGATCTAATATTT
genomic: AAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTT

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), 49 (downstream exon)
Score: 38

CATTACAATACTCACTGATTTAGCCAAGTCGATGAATAGGCTTGTTGCTGAAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTTCGTTGGCCTGCTGGAACCGATGGAGTTCTT


Block sizes: 37 (upstream exon), 43 (downstream exon)
Score: 8

CATTACAATACTCACTGATTTAGCCAAGTCGATGAATAGGCTTGTTGCTGAAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTTCGTTGGCCTGCTGGAACCGATGGAGTTCTT


Block sizes: 45 (upstream exon), 44 (downstream exon)
Score: 14

CATTACAATACTCACTGATTTAGCCAAGTCGATGAATAGGCTTGTTGCTGAAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTTCGTTGGCCTGCTGGAACCGATGGAGTTCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 31

CATTACAATACTCACTGATTTAGCCAAGTCGATGAATAGGCTTGTTGCTGAAGAGGCTGCTGGTGGCCTTTGGAATCTCTCTGTAGGCGAGGACCACAAGgttgttattc ... tgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTTCGTTGGCCTGCTGGAACCGATGGAGTTCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacttattattattgggatgtttttttgtgataattcaatggttgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTTCGTTGGCCTGCTGGAACCGATGGAGTTCTT
 gtataac  putative branch site (score: 31)
                      tttttttgtgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttattctatggatgctgattcattgcatgtataacttattattattgggatgtttttttgtgataattcaatggttgcacttcagGCGTCTATTGCAGTATCTGGTGGTATCAAGGCCCTGGTAGATCTAATATTTCGTTGGCCTGCTGGAACCGATGGAGTTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA