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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagtacaaggcatatttcctgattagttgcaatcatgctacagattactgatcggtatattgtatgcatgttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATTGCTCATTGCAAGACTTGACCATCGAGAAGCTATTGCCCGCTTGACTCTG

Basic information

species Zea mays
transcript GRMZM2G017654_T01
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017654_T01 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 3'ss of exon 22
gtaagagtacaaggcatatttcctgattagttgcaat-----------------catgctacagattactgatcggtata-ttgtatgcatgttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATTGCTCATTGCAAGACTTGACCATCGAGAAGCTATTGCCCGCTTGACTCTG
||||||  | |  |     |||||  ||  |  || |                 || | |||||| || |||    |  | ||| ||  |  ||  |  ||||||||||||| || ||||||||||||||||||||||||||||||| ||| |||| |||||||| |||||||| ||||||||||||||||| ||||| |||
gtaagaccaaagagttaccttcctttttgatgacattatataatatgaacatgacaggatacagaatattgagacatgcaattgcattgac-ttgactacagGAAATCTTCTCGGATAAATACAGCAATGGCTACCAATGGTTTAACGACACTGCTTATTGCAAGGCTTGACCACCGAGAAGCTATTGCCCGTTTGACACTG
















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|67013249|gb|CO441998.1|CO441998
EST:     CCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCAC                         GAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
genomic: CCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
EST: gi|16925145|gb|BM078213.1|BM078213
EST:     CTTGAAGATAATCAC                         GAGATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
genomic: CTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
EST: gi|32850766|gb|CD990447.1|CD990447
EST:     CCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCAC                         GAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
genomic: CCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
EST: gi|213179228|gb|FM184299.1|FM184299
EST:     CCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCAC                         GAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
genomic: CCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
EST: gi|67014005|gb|CO442754.1|CO442754
EST:     CAGAACAGTATTTTGGCCATATATTGGNACGCTT-CTTGAAGATA-TCAC                         GAAATCTTCTAGGCTAA-TACAGNCA-TGGCTA
genomic: CAGAACAGTATTTTGGCCATATATTGG-ACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAG-CAATGGCTA
EST: gi|67030562|gb|CO459311.1|CO459311
EST:     CCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCAC                         GAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT
genomic: CCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATT

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), 45 (downstream exon)
Score: 129

TGTTGAAAAAAGAGGCCATTCAGAAATTAGTGAAGTTCTTCCAAGATTGCCCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATTGCTCATTGCAAGACTTGACCATCGAGAAGCTATTGCCCGCTTGACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

TGTTGAAAAAAGAGGCCATTCAGAAATTAGTGAAGTTCTTCCAAGATTGCCCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATTGCTCATTGCAAGACTTGACCATCGAGAAGCTATTGCCCGCTTGACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

TGTTGAAAAAAGAGGCCATTCAGAAATTAGTGAAGTTCTTCCAAGATTGCCCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATTGCTCATTGCAAGACTTGACCATCGAGAAGCTATTGCCCGCTTGACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

TGTTGAAAAAAGAGGCCATTCAGAAATTAGTGAAGTTCTTCCAAGATTGCCCAGAACAGTATTTTGGCCATATATTGGACGCTTTCTTGAAGATAATCACgtaagagtac ... ttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATTGCTCATTGCAAGACTTGACCATCGAGAAGCTATTGCCCGCTTGACTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgcaatcatgctacagattactgatcggtatattgtatgcatgttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATTGCTCATTGCAAGACTTGACCATCGAGAAGCTATTGCCCGCTTGACTCTG
                    tactgat  putative branch site (score: 128)
                                           tgttttc  putative PPT
                              tatattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagtacaaggcatatttcctgattagttgcaatcatgctacagattactgatcggtatattgtatgcatgttttcggcagGAAATCTTCTAGGCTAAATACAGCAATGGCTACCAATGGTTTAACAACATTGCTCATTGCAAGACTTGACCATCGAGAAGCTATTGCCCGCTTGACTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC