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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatagtacatgtgacctaactcttttattgtattgtaacgttctgtgtctgttttgctaatctattcgagttctcactgtccttgtttattctag

Basic information

species Zea mays
transcript GRMZM2G083095_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 5'ss of exon 9
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatagtacatgtgacctaactcttttattgtattgta-acgttctgtgtctgttttgctaatctattcgagttctcactgtccttgtttattctag
||||||||| ||||||||||| |||||||| |||||||| || || |||||| | ||||||||||||||||||||||||||||| || ||||| ||||||||||  |  ||| ||   || |       || || |     | || | ||     | |||   ||    |   |    || |||||   ||||||| |   
AGGTGGAAACTCAGTGGCTACGGTTGTCTTAAGAGGCAGCACCGATAGTATATTGGATGATCTTGAAAGAGCTGTTGATGATGGTGTGAATACTTACAAGgtatg-actgtaaat-caacttcctgtcattgttttggaacatacatgctactcttatttaattagctaacaggttacctgactgttggtgtttatacag-

upper sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G07910.1 (Glycine max), 5'ss of exon 9
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatagtacatgtgacctaactc-ttttattgtattgtaacgttctgtgtctgttttgctaatctattcgagttctcactgtccttgtttattctag----------------------------------------------------------------------------------------
 ||||||||||| || || |||||||| ||  |||| |||||||| |||||||||||||||||||||||||| || |||||||| || || || |||||||||  | |  ||  | |  |   | |  | || |   | |    |        |  |  ||  |  |   |  ||  | |   ||   ||    |||  |                                                                                         
GGGTGGAAATTCTGTAGCCACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaattttcttatgtttcgctccattaatcttgtaaaaatagggcagcaaacctaagggttattgttacttatgacatttgtttgga-ttacacatttgaaggaattttatttttaaaaacaattttatgctttggctaattgtaatttgaaatactggttaatctttatctttacaattacttgtcag

upper sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G26920.1 (Glycine max), 5'ss of exon 9
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgta-tctatagtacatgtgacctaactcttttattgtattgtaacgttctgtgtctgttttgctaatctattcgagttctcactgtccttgtttattctag
 ||||||||||| |||||||||||||| ||  |||| |||||||| |||||||||||||||||||||||||| || |||||||| || || || ||||||||| | |     |  | |      | | ||  ||  | ||| |||  |   | |||| | |     || ||     || | |   |     |  |  |   
GGGTGGAAATTCTGTGGCTACTGTTGTTTTACGAGGAAGTACTGATAGTATACTAGATGATCTTGAAAGAGCAGTGGATGATGGAGTGAACACTTACAAGgtaatttccccaatgtttttttgtaattttgaatgatcttgaaacagtaattttctgatgtttctctccatcaatcttgtaaaaatagggctgcaaacct-

upper sequence: GRMZM2G083095_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 5'ss of exon 9
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgta---tctatagtacatgtg------------acctaactcttttattgtattgtaacgtt--ctgtgtc-tgttttgctaatctattcgagttct----cactgtccttgtttattctag-------------
||||||||| || ||    ||||| || ||  |||| |||||||| |||||| ||||||| ||||||||||| |||||||| || || ||||| |||||||||   | |||| |  ||| |            |  ||  | ||| |      || |  | |   ||  || | | || ||  | | || ||  | |    |  |    ||   |  | ||              
AGGTGGAAACTCCGTATGCACTGTGGTTTTACGAGGAAGTACTGATAGTATATTAGATGACCTTGAAAGAGCAGTTGATGACGGTGTGAATACATACAAGgtaaattttatattggatgggctggtcttgtaaatataggtttttgagcactatggagtggtggttgcatcatctcttacttttttgttggaaatttatgacgttaatattaggtgctttacatttcaatgccag

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|148978583|gb|EE026232.2|EE026232
EST:     AAAGAGCTGTTGATGATGGCGTCAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: AAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|113703848|gb|EE681352.1|EE681352
EST:     CTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: CTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|6626281|gb|AW257813.1|AW257813
EST:     TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCCGCAACAGAAATA
genomic: TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|60396537|gb|DN229406.1|DN229406
EST:     TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|60358886|gb|DN225859.1|DN225859
EST:     TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|24773918|gb|CA409172.1|CA409172
EST:     TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|148972050|gb|EE022890.2|EE022890
EST:     AATACGTACAAG                         TCAATGGGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: AATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|211337115|gb|FK966356.1|FK966356
EST:     CAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: CAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|91053532|gb|EB163950.1|EB163950
EST:     TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|110194417|gb|EC876315.1|EC876315
EST:     TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAG                         TCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
EST: gi|60337628|gb|DN204601.1|DN204601
EST:     TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGT---A-                         -C-A-----AGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA
genomic: TACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATA

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: 244

AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 147

AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 121

AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatag ... tttattctagTCAATGTGCAGGGACAGTAGGATAATTCCTGGTGCTGCTGCAACAGAAATAGAGCTGGCAAAGAGATTGAAGGAGTTCTCTTTGAAGGAAACAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTGGAAATTCAGTGGCTACTGTTGTCTTGAGAGGCAGTACTGACAGTATACTAGATGATCTTGAAAGAGCTGTTGATGATGGCGTCAATACGTACAAGgtatctatagtacatgtgacctaactcttttattgtattgtaacgttctgtgtctgttttgctaatctattcgagttctcactgtccttgtttattctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT