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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctccgtgctaaatcctactgttcaaatcctgctggccaactatataccctctctgtagggtttgctttttggtgagcggttgaatggttgcgt...

Basic information

species Zea mays
transcript GRMZM2G047590_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047590_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g56800.1 (Oryza sativa), 5'ss of exon 2
CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctccgt-----gctaaatcctactgttcaaatc---ctgctggc-caactatataccctctctgtagggtttgctttttggtgagcggttgaatggttgcgt
|| || ||||||||  |||||||| |||| || ||| ||||||||||||||||  ||||| | |||||||||| ||| |||||||| || |||||||| ||||||| | ||       ||||            ||  ||   ||| |||      | |||||     || |  | |||||||| || ||||||  ||| |        
CGGGCCCTCCGCGAGAAGATCGTCGCCGGGGAGCGCAAGTTCGAGGACGTCGCCACCGAGGAGTCCGACTGCAACTCCGCCAAGCGTGGGGGTGACCTAGgtcagtacgccacacgccgctacccatccacccccatgtcaatctgttggtgtgtttctatacagaa-ctatgagatttgctttctgatgagcgtctgatt--------

upper sequence: GRMZM2G047590_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G24140.1 (Glycine max), 5'ss of exon 1
CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctccgtgctaaatcctactgttcaaatcctgctggccaactatat--accctctctgtagggtttgctttttggtgagcggttgaatggttgcgt
   || ||||||||| | ||||| || ||  |   |   ||||||||| ||||  |      |||||| |||||||| ||||||||||| ||||| |||||||||| |        ||    || | || | ||          | | | ||  |     |   | | ||     ||| | ||   |||    || |   | 
AAGGCCCTCCGCGACGACATCGTTTCGGGCAAGGCCTCCTTCGAGGACATCGCCTCTCGCTTCTCCGATTGCAGCTCCGCCAAGCGCGGGGGTGATCTCGgtcagt-cgaaaaatgaatgtttattttttatatataaaaaaatagcaacattaaaaggtttaattgtgtacagatttggatgtatggtattctgatgaag-

upper sequence: GRMZM2G047590_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G05560.1 (Glycine max), 5'ss of exon 1
CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctccgtgctaaatcctactgttcaaatcctgctggccaactatataccctctctgtagggtttgctttttggtgagcggttgaatggttgcgt---
   || ||||||||| | ||||| || ||  |   |   || |||||| ||||  |      |||||| |||||||| ||||||||||||||||| |||||| |||         | |||  | ||  |  |||          ||   | |    | | |  ||  || |   | ||||   |   |||| | |    |   
AAGGCCCTCCGCGACGACATCGTTTCGGGCAAGGCCACTTTTGAGGACATCGCCTCTCGCTTCTCCGATTGCAGCTCCGCCAAGCGCGGCGGTGATCTCGgttagt--cgaaaaatgaatgtttcttatataatagcaa-aattaaaagttttaattgtgtaaagatttggacgtatggtattcttatgaaggatctgataat

upper sequence: GRMZM2G047590_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv04s0023g03190.t01 (Vitis vinifera), 5'ss of exon 1
CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctccgtgctaaatcctactgttcaaatcctgctggccaactatataccctctctgtagggtttgctttttggtgagcggttgaatggttgcgt---
   ||  | |||||| | ||| | || ||  |     |||||   ||||||||| |  | | |||||| |||||||| |||||||||||||| || ||||||| ||  |    |||  |  |   | || |  | || |||      |   |    |     |||||||| |  |   |    |  ||     | || |    
AAGGCCATTCGCGACGACATCATTTCTGGCAAATCTAAGTTCTCCGACGTCGCTTCTCAAATCTCCGATTGCAGCTCTGCCAAGCGCGGCGGCGATCTCGgtcggtttttatagctctactc---tctttatcttcttctgttttgattggtttttttggattagggttttcactcctgccttctctttggatgctgagaaaa

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|110952699|gb|EE172751.1|EE172751
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|19351247|gb|BM895779.1|BM895779
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GATCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|211507708|gb|FL330169.1|FL330169
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|211277846|gb|FL334393.1|FL334393
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|211015284|gb|FL323181.1|FL323181
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|87152470|gb|DY397259.1|DY397259
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GATCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|149095238|gb|EE180863.2|EE180863
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|31558742|gb|CD527954.1|CD527954
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|21432235|gb|BQ547725.1|BQ547725
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGTGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|8665793|gb|BE186609.1|BE186609
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGTGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|31558741|gb|CD527953.1|CD527953
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|149083431|gb|EE172752.2|EE172752
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|9028758|gb|BE238798.1|BE238798
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGTGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|211195923|gb|FL345932.1|FL345932
EST:     CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
EST: gi|211026252|gb|FL455125.1|FL455125
EST:     CGCTGCCGAGAACTCCGACTGCAGYTCGGCCAAGCGCGGCGGTGACCTCG                         GTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG
genomic: CGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTG

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), 46 (downstream exon)
Score: 94

CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTGCTCTGAAGGTCGGGGAGATCAGCGACGTGGTTGATACAGAGAGCGGGGT


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 46

CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTGCTCTGAAGGTCGGGGAGATCAGCGACGTGGTTGATACAGAGAGCGGGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTGCTCTGAAGGTCGGGGAGATCAGCGACGTGGTTGATACAGAGAGCGGGGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 50

CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctc ... tttgttgcagGTTCATTTGGGAGGGGTAAGATGCAGAAGCCTTTTGAGAAGGCCGCGTTTGCTCTGAAGGTCGGGGAGATCAGCGACGTGGTTGATACAGAGAGCGGGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGCGCTCCGCGACCAGATCGTCTCCGGTGACCGCGAGTTCGAGGACGTCGCTGCCGAGAACTCCGACTGCAGCTCGGCCAAGCGCGGCGGTGACCTCGgtcagtgctccgtgctaaatcctactgttcaaatcctgctggccaactatataccctctctgtagggtttgctttttggtgagcggttgaatggttgcgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC