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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataactttgttcttataattacactatctgtgttatttctgacagcaatatgatatttattttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG

Basic information

species Zea mays
transcript GRMZM2G154165_T04
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA16G08410.1 (Glycine max), 3'ss of exon 17
--------------------------------gtataactttgttcttataattacactatc---tgtgttatttctgacagcaatatgatatttattttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG
                                |   || |   | ||  | |  |||||||    |||     |  |||     |||  ||     || | |||||| |||||||||||||||||||| || || |||||||| ||||| ||| ||||||| ||||| ||||||||||| ||||||||||| || ||||| || |
ttcctaagattacatttcttacccctaatgaagagcaaataaatgctggttaaaacactattaaatgtcgagatattgatgctcataaaat-----ttcttgtagGTGGCATCTTGGTGGGACTATGGATACCAAACAACTGCCATGGCTAACCGAACTGTCATTGTTGACAATAATACCTGGAATAACACACATATTGCTACTG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA01G01270.1 (Glycine max), 3'ss of exon 17
---------------------------------gtataactttgttcttataattacactatctgtgttatttctgacagcaatatgatatttattttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG
                                 | | || |   | ||  | |  ||||  | |   |  |     |  |  | || | |||| ||   |||||| || ||||||||||||||||| || ||||||||||| ||||| ||| ||||||| ||||| || |||||||| ||||||||||| || ||||| || |
ctccttaagattatttttcttaccccaaatgaagaacaaataaatgctggttaaaacacattataaatgttgagatattgacacataaaatttctt---gtagGTGGCTTCTTGGTGGGACTATGGCTACCAGACAACTGCCATGGCTAACCGAACTGTCATTGTTGATAATAATACCTGGAATAACACACATATTGCTACTG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 15
lower sequence: AT5G19690.1 (Arabidopsis thaliana), 3'ss of exon 17
----------------------------------------------------------------gtataactttgttcttata-attacactatctgtgttatttctgacagcaatatgatatttattttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG
                                                                ||||||  |   | | ||| || |   |  ||| |||   | || ||  ||||  ||       ||||||||| ||||| ||||||||||||||||||||||| || || ||||| || |||||||| ||||| ||||| || ||||||||||| || ||||||||||| |
gtaagttttttcaacaaaaacaagtcagtttttagttcctgttaagcatcatcctttggtagaggtataagctgtctttaatatatgaagttgcctgagtttgatttg-caaaaataaaat------cttggtagGTGGCATCATGGTGGGACTATGGTTATCAGACGACAGCTATGGCTAATAGAACTGTGATTGTTGACAACAACACATGGAATAATACTCACATTGCAACTG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 15
lower sequence: Vv11s0016g03320.t01 (Vitis vinifera), 3'ss of exon 17
---------------------------gtataactttgttcttataattacactatctgtgttatttctgacagcaatatgatattta----ttttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG
                              || ||       |||  |||  ||||    | ||||   || |  | | |  ||||      || | | |||||||||||||||||||||||||||| || || ||||| ||||| ||| | ||||||||||||||||||||||| ||||||||||| || |||||||| |
tagcaaatcatttctgatagagtttctagctagctaatgcagtatccttaacctattgaaggtattaaagaaattagt-tcttattggaaacttcttgcagGTTGCATCTTGGTGGGACTATGGTTACCAAACTACTGCTATGGCTAACCGGACTGTTATTGTGGACAATAATACCTGGAATAACACTCATATTGCAACTG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 15
lower sequence: PP1S404_37V6.1 (Physcomitrella patens), 3'ss of exon 17
----------------------------gtataactttgttcttataat-tacact-atctgtgttatttctgacagcaatatgatatttattttggt-agGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG
                            ||   | || |  |||    | |  ||| |    |||| |   ||     ||   | | ||| | |||   |||| || || |||||||| ||||| ||||| |||||||||||||| ||||||||||| ||||||||||| || || ||||||||||||||||| || ||||
tcgcatgtttgggttgatcaaccgtcaggtcggaattaggcctttcgttctggactcaggattgttttcattgctcttaacgcg-tgtttgtgttgaccagGTGGCGTCCTGGTGGGATTATGGATATCAAACAACTGCAATGGCGAACAGAACTGTGATTGTGGACAACAACACGTGGAATAACACGCACATAGCTACAG

upper sequence: GRMZM2G154165_T03 (Zea mays), 3'ss of exon 15
lower sequence: EFJ15189 (Selaginella moellendorffii), 3'ss of exon 17
gtataactttgttcttataattacactatctgtgttatttctgacagcaatatgatatttattttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG
               | |  ||     |  ||| ||    |||  |   ||    ||   | |   | |||| || || |||||||| ||||| ||||| || || |||||||||||||| ||||| ||||| ||||| || |||||||| || |||||||| || || |
--------------gtctgtttgtggcacatgtatt--ccctgctaaagattcattaagcact---gaagGTGGCGTCGTGGTGGGATTATGGCTATCAAACGACAGCAATGGCAAACAGGACTGTCATTGTAGACAACAACACATGGAACAATACGCACATAGCCACCG

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|67014712|gb|CO443461.1|CO443461
EST:     TCCGCGAAGCTTATGGATGGCTGCGCCATAACACAGATGCAGATGACAAG                         GTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGA
genomic: TCCGCGAAGCTTATGGATGGCTGCGCCATAACACAGATGCAGATGACAAGgtataacttt ... attttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGA
EST: gi|33093933|gb|CF053927.1|CF053927
EST:     TCCGCGAAGCTTATGGATGGCTGCGCCATAACACAGATGCAGATGACAAG                         GTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGA
genomic: TCCGCGAAGCTTATGGATGGCTGCGCCATAACACAGATGCAGATGACAAGgtataacttt ... attttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGA

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), 48 (downstream exon)
Score: 101

AATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCGAAGCTTATGGATGGCTGCGCCATAACACAGATGCAGATGACAAGgtataacttt ... attttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 16

AATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCGAAGCTTATGGATGGCTGCGCCATAACACAGATGCAGATGACAAGgtataacttt ... attttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG


Block sizes: 34 (upstream exon), 46 (downstream exon)
Score: 7

AATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCGAAGCTTATGGATGGCTGCGCCATAACACAGATGCAGATGACAAGgtataacttt ... attttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 68

AATTGTGCTAACATCTCGTTCACATGATGGGTTTCATGTTTTTGATGATTTCCGCGAAGCTTATGGATGGCTGCGCCATAACACAGATGCAGATGACAAGgtataacttt ... attttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataattacactatctgtgttatttctgacagcaatatgatatttattttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG
                       ttctgac  putative branch site (score: 68)
                                          tttatttt  putative PPT
                                 aatatgatatttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataactttgttcttataattacactatctgtgttatttctgacagcaatatgatatttattttggtagGTTGCATCTTGGTGGGACTATGGTTATCAGACAACTGCAATGGCAAACAGAACTGTTATTGTGGACAATAATACATGGAATAACACGCACATTGCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA