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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatatagcatatccagtctgctgtgcacatgaattatacaatgaaagctcccttgtgtaatgcaacttccattagtgtcactatgcacactatgt...

Basic information

species Zea mays
transcript GRMZM2G011923_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 5
CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatatagcatatccagtctgctgtgcacatgaattatacaatgaaagctcccttgtgtaatgc--aacttc----cattagtgtcactatgcacactatgt---------------------
| |||| ||||| |||||||| |||||||||||| | ||||| |||||  ||||||| || ||||| ||||||||||| || ||||||||||| || ||||||| ||  |    |||      | |||||||||||  ||  || || || | | |  | || | |    || | |    ||  | |||  | ||||| |||  |                      
CATTAGAAAGCTCTGCAAGCCTTTGGAAGAGGATGCTTTCAGACCAGTGCTGCACCATTACGATGGTCCAAAGTTTCGTCTTGAGCTCTCCATAGCTGAGgtatgtaggt----tattactattactgtgcacatggtttg-actat-aatgttactatatgcagtattgaattgcacaacaaaaatgtggccatgcaaactgagcaatatcatcttaaatttacag

upper sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 5
CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatatagcatatccagtctgctgtgcacatgaattatacaatgaaagctcccttgtgtaatgcaacttccattagtgtcactatgcacactatgt-------------------
 || |||||||| |||||| | |||||||| ||||| ||||||||||| ||||| || ||||| || ||||||||||| || || || ||  |  | |||||||  |   |  ||  | | | |    |  | | |||| || | |||| |  |   ||||          |||  | | ||      || |   | |                     
TGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGACGGGCCAAAGTTTCGTCTTGAACTGTCAGTTCCAGAGgtatg-aaggaatattgctattttaaacta-aaaagaatcattccatgaca-ttgatttgtccctgttggtttctgtcattgatggagtggaatttgttattgttattggatattgcag

upper sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 5
CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatatagcatatccagtctgctgtgc--acatgaattatacaatgaaa-----------------gctcccttgtgtaatgcaact---tccattagtgtcactatgcacactatgt
 || |||||||| |||||| | |||||||| ||||| ||||||||||| ||||| || |||||||| ||||||||||| || ||||| ||  |  | |||||||  |   |   |  | | | |  |   |  | | |||| ||   |||| |                 | | |  | | | ||| |      |   ||| ||| | |    | | |    
TGTCAGGAAGCTCTGCAAGGCATTGGAAGAAGATTCTTTCAGGCCAGTATTGCATCATTATGATGGGCCAAAGTTTCGTCTTGAGCTGTCAGTTCCAGAGgtatg-aaggaatgttgctatttttttaaactaaaaagaatcatttcatgacattgatttgtcaccgttggtttctgtctttgatggagtggaatttgttattgttattggatatattgcag

upper sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 5
CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatatagcatatccagtctgctgtgcacatgaattatacaatgaaagctcccttgtgtaatgcaacttccatta-gtgtcactatgcacactatgt-------
 || |||||  | |||||  | ||||||||||| ||||||||||||||  | |||||||||||||| ||||| || ||||| ||||||||  |  | |||||   | |    ||||| |  | ||       ||  ||| | | ||| ||           | ||   ||  |  |||  ||||||  |||   |   ||        
AGTGAGGAAAATCTGCAAAGCCTTGGAAGAGGACTCCTTCAGGCCAGTACTTCACCACTATGATGGTCCAAAATTCCGCCTTGAGCTCTCTGTTCCTGAGgtgcgtgtc---catatacgttttgtgaatgtcagtaataagataattaag-----tgaacggaaaataatctgtattgtgtgtcatcatgtgaaaattggaacttgg

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|22490259|gb|BU050182.1|BU050182
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|18655190|gb|BM499995.1|BM499995
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|149107938|gb|EE292294.2|EE292294
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|31351065|gb|CD435422.1|CD435422
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|31352279|gb|CD436636.1|CD436636
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|31352997|gb|CD437354.1|CD437354
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|87152915|gb|DY397704.1|DY397704
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|31351326|gb|CD435683.1|CD435683
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|148982112|gb|EE028161.2|EE028161
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|37399688|gb|CF637177.1|CF637177
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|211109604|gb|FL216793.1|FL216793
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|60350260|gb|DN217233.1|DN217233
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|78087740|gb|DV516133.1|DV516133
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|40303492|gb|CK347879.1|CK347879
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|45567374|gb|CK985540.1|CK985540
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|60346554|gb|DN213527.1|DN213527
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|113701892|gb|EE679396.1|EE679396
EST:     CACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: CACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|31352510|gb|CD436867.1|CD436867
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|60338925|gb|DN205898.1|DN205898
EST:     CCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: CCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|149082225|gb|EE171408.2|EE171408
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATTTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|60401294|gb|DN234101.1|DN234101
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|211413346|gb|FL280968.1|FL280968
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTTGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTA
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTA
EST: gi|60358053|gb|DN225026.1|DN225026
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
EST: gi|29544380|gb|CB604760.1|CB604760
EST:     TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAG                         ACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC
genomic: TGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGC

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: 574

CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGCTGCCTCGTGAGGTTCTAGTAAATATCAATCATCCTTGTATGTTCTGTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 366

CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGCTGCCTCGTGAGGTTCTAGTAAATATCAATCATCCTTGTATGTTCTGTAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 240

CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGCTGCCTCGTGAGGTTCTAGTAAATATCAATCATCCTTGTATGTTCTGTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 534

CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatat ... aaatttgcagACCCTGTCCCTGCTAGACCTATGCGAGAAGGAAGGCATCTGAGCTGTTGGCTGCCTCGTGAGGTTCTAGTAAATATCAATCATCCTTGTATGTTCTGTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTCAGGCCAGTTTTGCACCACTATGATGGCCCAAAGTTTCGCCTCGAGCTCTCCATCGCGGAGgtatatatatagcatatccagtctgctgtgcacatgaattatacaatgaaagctcccttgtgtaatgcaacttccattagtgtcactatgcacactatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctccctt