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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacag

Basic information

species Zea mays
transcript GRMZM2G000645_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 15
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctc-----gaaaacatttcttctgtt--taaattctctatatgggcacttcatgt--catgacttcaattgcttacatagttataagctttatacttacag
||||||| | |||||||||||| | || || || |||||||||||||||||||| |||||||| ||||| |||||||| || |||||||||||||| |||||| |||| || |||||      | ||  ||| || ||||  |  ||| |||||    | | ||  ||    |  | || |     ||  | | ||| |                
TCATGAGGTTAATGAGCGAGTGCGGACAGGGATCTGGGTTGGAGACTGCTTTATTTATAACAATTCATCATGGCGCCTGAACTATTGTGTTGGTGGCGAGgtatatattgtgtgctccatgcaagaatttttattttgttaatgtattttctattgtagtattttgtgcactacaaatttatcccgttgtacatttacag---------------

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 15
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgc--ttacatagttataagctttatacttacag------
 ||||| || ||||| || || ||||| || || |||||||| || ||||||||||| ||||| || || ||| | || ||||| ||||||||||||||||||   |   | | | |    | ||||||  | |  |||     | |     |  ||    |    ||| |||      | | | |  |  | || | ||  |||         
ACATGAAATGAATGAACGTGTCAGAACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATTCCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattg-aactacaaggatcatgagacatcttgatgcataatgattatgaatttag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 15
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctcgaaaacatttcttctg--tttaaattctctatatgggcacttcat-gtcatgacttcaat-tgcttacatagttataagctttatacttacag--------------------------------------------------
|||||| || ||||| || || || || || || |||||||| || || |||||||| ||||| || || ||| | || || |||||||||||||||||||||  ||   | | | |    | |||         |  | |||   |   ||  | |||  |  ||||   |||  | || | |   | || | |  | |||| |||  |                                                  
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAACAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 15
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgc--ttacatagttataagctttatacttacag------
 ||||| || ||||| || || || || || || |||||||| || ||||||||||| |||||  | || ||| | || ||||| ||||||||||||||||||   |   | | | |    | ||||||  | || |||       | ||    |||  |      ||| | |      | | | |  |  |  | | ||  |||         
ACATGAAATGAATGAACGTGTCAGGACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATACCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttttcccttctagatttctagt-ttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagacatcttgatacataatgattatgaatttag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 19
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacag
  |||| | |||||| || ||  | |||||  | |||||||| || || |||||||||| |||||| || ||| | || ||||| |||||||||||||||||||   |  | | || |       || ||      |||   | ||| |      ||  |||  | | |   |||   |||             ||||| ||||||
CAATGAAACCAATGAACGTGTTCGGACTGGCTTATGGGTTGGGGATTGTTTTATCTATACCAACTCTTCTTGGAGGCTTAATTACTGTGTTGGTGGTGAGgtaaggctcattt-ctagg------tttttggaaagaaacgttttatgttttttattt-tgttgtaattgagattcagtactcc--------tcttata-ttacag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 15
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtc-atgacttcaattgcttacatagttataagctttatacttacag-------
 |||||||  |||||  |||| |||||||| || |||||||||||||| || || || |||||||| || ||||| || ||||| ||||||||||| ||||||  | |    ||  |    ||  || |  ||     ||| || ||||| |||  | || || ||  | |  ||| |||  |   || |  | |  |||   | |        
CCATGAGACAAATGAAAGAGTTAGAACTGGTATATGGGTTGGAGACTGTTTCATTTACAACAACTCCTCTTGGCGGCTTAATTACTGTGTTGGTGGCGAGgtat-tgtgtattgtcc----acccttgtcttgaaagtatt-tccatatgtgcagatgatatccatttcatggatttcttgga-gcttttttgttaaataaccatatgttccag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 15
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgta-aatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacag
 ||||| || ||||||||||| ||||||||||| |||||||| |||||||| || || || ||||| || ||||| || || ||||||||||||||||||||| || | |||    || |             |||  | |||| |||||  |  ||||||   | |  | || |    ||   | || | |   | ||  || |||
CCATGAAATAAATGAGCGAGTCAGAACTGGAATATGGGTTGGGGACTGCTTCATTTACAATAACTCCTCTTGGCGACTTAACTATTGTGTTGGTGGTGAGgtataagagagttgattccag------------gttgtatttctatatatatgatcttcattctaagg-tgcagtcatata---aattgttaatgtgatgatttcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 15
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 5'ss of exon 15
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacag
||||||  |    ||||| ||  | || || |||||||| || ||||| || || |||||||||||| |||||||| | || || ||||||||||| || |||| | | |    ||   | | | ||   |  ||   |||    | |||        || | |    |||| |     |      | |    |||      ||||
TCATGAAGTATCGGAGCGTGTTCGTACGGGTATTTGGGTGGGCGACTGTTTCATATATAACAACTCAGCGTGGCGCTTGAACTACTGTGTTGGTGGAGAAgtaagttttgatcacttcgagaaagttaagc-attctcatttgtgacatgca-gtagtattttagcggttcactcatacaatcttctgttgcattttcttccacag

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|18965038|gb|BM661357.1|BM661357
EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
EST: gi|19351531|gb|BM896063.1|BM896063
EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
EST: gi|89106492|gb|DY576709.1|DY576709
EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
EST: gi|22490520|gb|BU050443.1|BU050443
EST:     TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAG                         GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT
genomic: TTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATT

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: 195

TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 87

TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 74

TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatag ... atacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAGATCAATGAGCGAGTGAGAACTGGAATTTGGGTTGGAGACTGCTTTATCTATAACAACTCATCGTGGCGCCTAAATTATTGTGTTGGTGGTGAGgtaaatatagtctgctcgaaaacatttcttctgtttaaattctctatatgggcacttcatgtcatgacttcaattgcttacatagttataagctttatacttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG