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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacacccttttcctgaactcttgcatgtgttgcatcagtagtagttgtttcttattgcaagttgcttctgataaataagcacattggccttgtctatg...

Basic information

species Zea mays
transcript GRMZM2G157722_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157722_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g36790.1 (Oryza sativa), 5'ss of exon 1
AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacacccttttcctgaactcttgcatgtgttgcatcagtagtagttgtttcttattgcaagttgcttctgataaataagcacattggccttgtctatg----
 |||||||||||||     ||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||| |||  |  ||| || |||||||||||||||||  | ||    |||||  |||||||| | | || ||||| |   | | | | |  |     ||     
GAGGAGGAGCGGTGGTAACGTGGAGAAGGTGGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCAGCAGCTAGATCTCGTGCCCGGAAGCAGgtcatacctctgccctaaattcttgcatgtgttgcatatgcagc---tgtttgctattgcaaatgg-ttgtgatagaaggggaaaatagtatcacaaatctggt

upper sequence: GRMZM2G157722_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S49_161V6.1 (Physcomitrella patens), 5'ss of exon 3
AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacacccttttcctgaactcttgcatgtgttgcatcagtagtagttgtttcttattgcaagttgcttctgataaataagcacattggccttgtctatg----------------------------------------
 ||| ||   | ||  |  |||||||| || |||||  |||||||| || ||||||||||||||||||| || || ||  | || || ||||| ||||||||  ||   ||    ||       |   | |  |  |  |  |||     | | | | |  ||  ||    |   | | |||     |    ||     |                                        
GAGGGGGTCGGATGGTGCAGTGGAGAAAGTAGTGGAAAGGCGGCAGCGGCGGATGATCAAGAACAGGGAATCGGCGGCGCGGTCTCGGGCCCGGAAGCAGgtatcagagttgcgttggggaagggggaggggggatttgg--gtaagcaatgcatgtggggaggggcg---gtggagtgagcgtgcggattgtgggcgagaggcggtggatcgctaaagatgtgtgatgtagcactgcag

upper sequence: GRMZM2G157722_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ21671 (Selaginella moellendorffii), 5'ss of exon 1
AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacacccttttcctgaactcttgcatgtgttgcatcagtagtagttgtttcttattgcaagttgcttctgataaataagcacattggccttgtctatg
 ||||     |  |||    |||||||| ||||||||||| ||||| ||||||||||||||||| |||| || || ||  |||| || ||  | || |||||| |    | || |       |   |   | ||  |   | || | | ||| ||   || ||||  || |    |                        
GAGGATCCTGGACGCGCCGCTGGAGAAGATTGTGGAGCGGAGGCAGCGGAGGATGATCAAGAACCGGGAATCGGCGGCGCGATCGCGAGCGAGGAAACAGgtc-cgtgatctttcaa-----tcaaaaaagctg-gttttttgtcgctctttgtttacgcgagttcgttgtctccag-----------------------

upper sequence: GRMZM2G157722_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ33828 (Selaginella moellendorffii), 5'ss of exon 2
AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacacccttttcctgaactcttgcatgtgttgcatcagtagtagttgtttcttattgcaagttgcttctgataaataagcacattggccttgtctatg
 ||||     |  |||    |||||||| ||||||||||| ||||| ||||||||||||||||| |||| || || ||  |||| || ||  | || |||||| |    | || |       |   |   | ||  |   | || | | ||| ||   || ||||  || |    |                        
GAGGATCCTGGACGCGCCGCTGGAGAAGATTGTGGAGCGGAGGCAGCGGAGGATGATCAAGAACCGGGAATCGGCGGCGCGATCGCGAGCGAGGAAACAGgtc-cgtgatctttcaa-----tcaaaaaggctg-gttttttgtcgctctttgtttacgcgagttcgttgtctccag-----------------------

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|71760129|gb|DR958066.1|DR958066
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|78117177|gb|DV535564.1|DV535564
EST:     GGATGACCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|93282472|gb|EB674736.1|EB674736
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|149072702|gb|EE160938.2|EE160938
EST:     GGATGATCAAGAACAGGGAGTTTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|71438068|gb|DR819118.1|DR819118
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGT
EST: gi|76283483|gb|DV023051.1|DV023051
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|88753387|gb|DY537528.1|DY537528
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|101385967|gb|EB815030.1|EB815030
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|71314118|gb|DR793675.1|DR793675
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|86470887|gb|DY237257.1|DY237257
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|71439337|gb|DR820387.1|DR820387
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAGGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
EST: gi|149113009|gb|EE295786.2|EE295786
EST:     GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAG                         GCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT
genomic: GGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAAT

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: 156

AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAATGCAGAATTGCAGAAGAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAATGCAGAATTGCAGAAGAAGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 145

AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAATGCAGAATTGCAGAAGAAGCAG


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

AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacaccct ... acgaatgtagGCTTATACAATGGAGTTGGAAGCCGAAGTTCAGAAACTGAAGGAACAAAATGCAGAATTGCAGAAGAAGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGAGGAGCGGTGCGGGTGTGGAGAAGGTTGTGGAGCGGCGGCAGAGGAGGATGATCAAGAACAGGGAGTCTGCAGCTAGATCCCGTGCCCGTAAGCAGgtcacacccttttcctgaactcttgcatgtgttgcatcagtagtagttgtttcttattgcaagttgcttctgataaataagcacattggccttgtctatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT