Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGCTGGACCAACTACCTGCGGCCGGACCTCAAGAGGGGCCTGCTCTCCGACGCCGAGGAGAAGCTCGTCATCGACCTGCATGCTCAGCTCGGCAACAGgtgccatgcatgcattgcatacccccacttctgaaaatgaactgtgttctgtatctatcttagattacatatttgaaggaaaataagcttagttttctttttttttaatgttcttaaaaaatgttag

Basic information

species Zea mays
transcript GRMZM2G106558_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106558_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g33150.1 (Oryza sativa), 5'ss of exon 2
TGCGCTGGACCAACTACCTGCGGCCGGACCTCAAGAGGGGCCTGCTCTCCGACGCCGAGGAGAAGCTCGTCATCGACCTGCATGCTCAGCTCGGCAACAGgtgccatgcatgcattgcatacccccacttctgaaaatgaactgtgttctgtatctatcttagattacatatttgaaggaaaataagcttagttttctttttttttaatgttcttaaaaaatgttag
| || ||||| |||||||| |||||||| ||||||||||| |||||||||||||||||||||||| ||||| ||||||| ||||| ||  | ||||| |||| | ||     |||||    || | ||   |    |  |  ||    ||| |  |||  || ||||  | ||| || | | |||     |      ||||| | ||        |||| |||||||
TACGGTGGACGAACTACCTCCGGCCGGATCTCAAGAGGGGGCTGCTCTCCGACGCCGAGGAGAAGATCGTCGTCGACCTACATGCCCAATTGGGCAATAGgtacgata---acattgt---cctcgacacgttgggacaacatgc---ctgaacgtatgataaatta-gttttttaatgtatatataacca------tttttatata-------caaaacatgttag
















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|211497011|gb|FL300938.1|FL300938
EST:     TGRACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499883|gb|FL300940.1|FL300940
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211497008|gb|FL300935.1|FL300935
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211497003|gb|FL300930.1|FL300930
EST:     AGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: -GGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|148936995|gb|EC881165.2|EC881165
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|148952168|gb|EC897965.2|EC897965
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|148946909|gb|EC892191.2|EC892191
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499893|gb|FL300950.1|FL300950
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499892|gb|FL300949.1|FL300949
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|148983172|gb|EE029113.2|EE029113
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499891|gb|FL300948.1|FL300948
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499888|gb|FL300945.1|FL300945
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|149084192|gb|EE173607.2|EE173607
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|148952214|gb|EC898015.2|EC898015
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499886|gb|FL300943.1|FL300943
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499894|gb|FL300951.1|FL300951
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211497004|gb|FL300931.1|FL300931
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|149111043|gb|EE294541.2|EE294541
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499885|gb|FL300942.1|FL300942
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211497010|gb|FL300937.1|FL300937
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|74235090|gb|DT643004.1|DT643004
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211497007|gb|FL300934.1|FL300934
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499887|gb|FL300944.1|FL300944
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|148951548|gb|EC897279.2|EC897279
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|149094896|gb|EE180475.2|EE180475
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499884|gb|FL300941.1|FL300941
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
EST: gi|211499896|gb|FL300953.1|FL300953
EST:     TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG
genomic: TGGACAGCGGAGGAGGACCAGAAGCTCGTCAGCTTCATCCTCGGCAACAGGCAGTGCTGCTGGCGCGCCGTGCCCAAGCTTGCCG

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 2 RNA-Seq libraries.


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 2

TGCGCTGGACCAACTACCTGCGGCCGGACCTCAAGAGGGGCCTGCTCTCCGACGCCGAGGAGAAGCTCGTCATCGACCTGCATGCTCAGCTCGGCAACAGgtgccatgca ... aaaatgttagGTGGTCAAAGATTGCGTCGCACATGCCAGGACGAACGGACAACGAGATTAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAGGAAGATGGGGATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

TGCGCTGGACCAACTACCTGCGGCCGGACCTCAAGAGGGGCCTGCTCTCCGACGCCGAGGAGAAGCTCGTCATCGACCTGCATGCTCAGCTCGGCAACAGgtgccatgca ... aaaatgttagGTGGTCAAAGATTGCGTCGCACATGCCAGGACGAACGGACAACGAGATTAAGAACCACTGGAACACCCACATCAAGAAGAAGCTCAGGAAGATGGGGATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGCTGGACCAACTACCTGCGGCCGGACCTCAAGAGGGGCCTGCTCTCCGACGCCGAGGAGAAGCTCGTCATCGACCTGCATGCTCAGCTCGGCAACAGgtgccatgcatgcattgcatacccccacttctgaaaatgaactgtgttctgtatctatcttagattacatatttgaaggaaaataagcttagttttctttttttttaatgttcttaaaaaatgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC