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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaaaacctttaactgccaattctttctagtttgagttgtttttgaaagtatttggtattctattatgtgt...

Basic information

species Zea mays
transcript GRMZM2G117544_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 5'ss of exon 5
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaa-aacctttaactgccaattctttctagtttga-gttgtt--tttgaaagtatttggt----attctattatgtgt--
||||||||| |||||||||||||| || || ||||||||||| ||||| ||||||||||||||||||||||||||||||| ||||||||||||    ||| || ||||   | |||||     ||| |||   | ||   |||  ||      |||     ||| | | ||  ||    ||| | ||  |||   
GGAACTAGCGAAAGATTTTGTGGTTTCTGGCACTGCTTCAGAATCACTATATGGTGCTTGTGAGTCCATGTATAAGCCAAGCATGgttagttt----acatgaaaactatctgcagaatggtattttacttatagtttggtctccttgagcactgtaaacatgacatttttctgtcacaattttctttggtgaag

upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA14G24270.3 (Glycine max), 5'ss of exon 4
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaaa-acctttaactgccaattctttctagtttgagttgtttttgaaagtatttggtattctattatgtgt
||| || |||||||||||||| || || || ||||| || ||||| || ||||||||||||||| | |||| ||||||  |||||||  ||  |   ||  |     |   |   |     |   | | ||  | |  | | |      | ||    | || | | | | | | || |    |   
GGAGCTTGCAAAAGATTTTGTTGTTTCTGGCACTGCATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcacaaaacttgtttgttttttgtggttttgcaaattaatgt-agtcgtgttttaccatacttaacatggataatttctagcaatcaacccagaaa

upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G11930.1 (Glycine max), 5'ss of exon 3
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaaaacctttaactgccaattctttctagtttgagttgtttttgaaagtatttggtattctattatgtgt------------
|||||| |||||||||||||  ||  | || ||||| || ||||| |||||||||||||||||||| |||| ||||||  |||||||| || ||          || || ||        ||||||| || || || |||     ||      ||  || |  || |   |||| | || |||||            
GGAACTTGCAAAAGATTTTGCAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctc--------gaaattcaatttgttg--cctttaa-tgtcactttttttagaatttgcaaattcctgcatttagtctatattttgtt-tgtgttgcttgagtttt

upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G42830.1 (Glycine max), 5'ss of exon 3
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaaaacctttaactgccaattctttctagtttgagttgtttttgaaagtat-ttggtattctattatgtgt------
|||||| |||||||||||||| ||  | || ||||| || ||||| |||||||||||||||||||| |||| ||||||  |||||||| || ||   |  |   || | | | |     |  ||   ||     || |||  | ||||     ||  || |  ||| |   |||| | || ||| |      
GGAACTTGCAAAAGATTTTGTAGTGGCTGGCACTGCATCCGAGTCTCTTTATGGTGCTTGTGAGTCAATGTTTAAGCCTGACATGgtttgtctcgaaattc---aatttgttgcctttgatgtt--gcttttttttttttagaatttgcaa-attcctgcagttatatctatattttgtt-tgtattgcttg

upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA13G10130.1 (Glycine max), 5'ss of exon 4
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaaaacctttaact------gccaattctttctagtttgagttgt-ttttgaaagtatttggtattctattatgtgt
||| || |||||||||||||| || || || ||||| || ||||| || ||||||||||||||| | |||| ||||||  |||||||| ||  |   | |    |||| | |       |  |||   |        |||     ||  || ||  |  |  ||| ||  |   | || |  |   ||    
GGAGCTTGCAAAAGATTTTGTTGTTTCTGGGACTGCATCTGAGTCTCTGTATGGTGCTTGTGAGGCGATGTTTAAGCCTGACATGgttggtccc---aaagactaacttgttttgtcttatatttggttttgtgaatcaacatagtcgtgtgtgtatcatacttttaatatggatagtttcttgcaat----

upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G21720.1 (Arabidopsis thaliana), 5'ss of exon 5
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttaca-cgagaactcgatacagaaaacctttaactgccaattctttcta-gtttgagttgtttt-tgaaagtatttggtattctattatgtgt
 ||  |||| ||||||||||| || || || ||||||||||| ||||| ||||| ||||||||| | ||||| |||||| | |||||| |     | ||| |   | |          | |  | ||| | || |   |    | | || | ||      |  | |  ||  | | | |  || ||  
AGAGTTAGCTAAAGATTTTGTTGTATCTGGAACTGCTTCAGAATCACTCTATGGAGCTTGTGAGGCAATGTACAAGCCAGATATGgtttgcccgctaacaacctcatcatctcttgttatatttctaaatcccgacaatgaaaatgcttaaattaccacatctaggcgtt--gcagtttggtaggtt-

upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G77440.1 (Arabidopsis thaliana), 5'ss of exon 5
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaaaacctttaactgccaattctttctagtttgagttgtttttgaaagtatttggtat--tctattatgtgt------
|||  |||| ||||||||||| ||||| || ||||||||||| || || |||||||| |||||  ||||||  || ||| | |||||  ||  |||     || |||| | |   | |  |  || ||||   || ||  | | | || |||  |      |  ||||||||   ||  | || |||      
GGAGTTAGCTAAAGATTTTGTTGTCTCGGGAACTGCTTCAGAATCTCTATATGGTGCCTGTGAAGCCATGTTCAAACCAGATATGgtatgtgccttc---tgaaaacttgtttttgtac-cgattcactg--gatact--caaatgtgtgtttatcacctgaaaatttggtaggatcattcatatgtaagtat

upper sequence: GRMZM2G117544_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S138_33V6.1 (Physcomitrella patens), 5'ss of exon 6
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaaaacctttaactgccaat-tctttctagtttgagttgtttttgaaagta---tttggtattctattatgtgt--------------------------------
| || | ||||| |||||||||||||| || ||||||||||||||  | |||||||| || || || ||||| || ||  |  ||||  | |  |  |    | |        |    |   ||||  |  || |  ||||  ||||     | | || |  || |   ||  ||  |  | |  |||                                 
GCAATTGGCAAAGGATTTTGTGGTCTCTGGAACTGCTTCAGAGTCTTTATATGGTGCCTGCGAATCTATGTACAAACCTGATTTGgtatgctaatccaattcatactgaatcgcgctgattatttattttgcattacctttggagttcttagtatcttggtgagcacgtttctgtgctgaactg-gtgcttacaagttgtatgctccctttcttttttcag

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|32844693|gb|CD984374.1|CD984374
EST:     CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAAGCATCTGGT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
EST: gi|88758274|gb|DY542415.1|DY542415
EST:     CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
EST: gi|94476825|gb|EB705783.1|EB705783
EST:     CTTCAGAGTCACTTTATGGTGGTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
EST: gi|32848246|gb|CD987927.1|CD987927
EST:     CTTCAGAGTCAGTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAAGCATCTGTT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
EST: gi|32844036|gb|CD983717.1|CD983717
EST:     CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAAGCATCTGTT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
EST: gi|161592540|gb|EY962985.1|EY962985
EST:     TTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGACCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTG
genomic: TTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAG-CCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTG
EST: gi|211034562|gb|FL157508.1|FL157508
EST:     CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAAGCATCTGTT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
EST: gi|32845419|gb|CD985100.1|CD985100
EST:     CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAAGCATCTGTT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
EST: gi|30088206|gb|CB886411.1|CB886411
EST:     CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
EST: gi|88758273|gb|DY542414.1|DY542414
EST:     CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATG                         GAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT
genomic: CTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTT

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), 47 (downstream exon)
Score: 139

GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 70

GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttct ... tggtatgaagGAACCCGAAGAACTTTTCGAGACAATCTCGCAAGCATTGCAGGCATCTGTTGATCGCGACTGCCTCAGCGGCTGGGGAGGTTATGTTCTTGTTGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAACTAGCAAAAGATTTTGTGGTCTCCGGTACTGCTTCAGAGTCACTTTATGGTGCTTGTGAGTCCATGTATAAGCCAAACATGgttagtttctttacacgagaactcgatacagaaaacctttaactgccaattctttctagtttgagttgtttttgaaagtatttggtattctattatgtgt

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