Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggctatgacacattgttgctcaaatgttgtattaatgtataatcttatgtgatacacttctcatatatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAATATCACAGGGATGAGCAAAGGGATGTTTCCAGGATTGTGGCCTTTGAAG

Basic information

species Zea mays
transcript GRMZM2G146951_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146951_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g17370.1 (Oryza sativa), 3'ss of exon 3
gtaagtggctatgacacattgttgctcaaatgttgtattaatgtataat-cttatgtgatacacttctca-------------tatatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAATATCACAGGGATGAGCAAAGGGATGTTTCCAGGATTGTGGCCTTTGAAG
|||||||  ||      | | ||| ||| ||| | |   |||| | | | ||||| |  | |||||                 | || |||||||||||| ||||||||   |||||| ||||||||| |||| ||||| ||||| |||||||||||||  |||||||||||||| ||||| || || |||||||
gtaagtg--taactttgagtattgatcacatgctatgaaaatgcaaagttcttatatcgtgcactttcttccctttttctgtttgtacttggcagAGCAAGGATGAAAAGAGCTTCATTCACAACCATTTATCATTTACTGTGAAGTATCACAGGGATGCCCAAAGGGATGTTTCTAGGATAGTTGCATTTGAAG
















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|78115833|gb|DV534221.1|DV534221
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|149012081|gb|EE042501.2|EE042501
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|22491002|gb|BU050925.1|BU050925
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|31353915|gb|CD438272.1|CD438272
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|149095226|gb|EE180848.2|EE180848
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCA
EST: gi|148999936|gb|EE036993.2|EE036993
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|148971253|gb|EE022114.2|EE022114
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|149080734|gb|EE169796.2|EE169796
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|91871350|gb|EB401373.1|EB401373
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|19437149|gb|BM953559.1|BM953559
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGCGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|148959757|gb|EC905651.2|EC905651
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
EST: gi|149023680|gb|EE045933.2|EE045933
EST:     ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGG                         AGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA
genomic: ATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAA

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), 49 (downstream exon)
Score: 247

CAACCTACCTTTAGTCGTTCCTATTCAAAGAGTGGATCAAGAAGGTGCATATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAATATCACAGGGATGAGCAAAGGGATGTTTCCAGGATTGTGGCCTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 302

CAACCTACCTTTAGTCGTTCCTATTCAAAGAGTGGATCAAGAAGGTGCATATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAATATCACAGGGATGAGCAAAGGGATGTTTCCAGGATTGTGGCCTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 325

CAACCTACCTTTAGTCGTTCCTATTCAAAGAGTGGATCAAGAAGGTGCATATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAATATCACAGGGATGAGCAAAGGGATGTTTCCAGGATTGTGGCCTTTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1434

CAACCTACCTTTAGTCGTTCCTATTCAAAGAGTGGATCAAGAAGGTGCATATTTCTATCAACATGGATTCCATGTTGGGGCCAAAGGAAAATATTCAGGGgtaagtggct ... tatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAATATCACAGGGATGAGCAAAGGGATGTTTCCAGGATTGTGGCCTTTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatgttgtattaatgtataatcttatgtgatacacttctcatatatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAATATCACAGGGATGAGCAAAGGGATGTTTCCAGGATTGTGGCCTTTGAAG
         tattaat  putative branch site (score: 1434)
      ttgtattaatgtataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggctatgacacattgttgctcaaatgttgtattaatgtataatcttatgtgatacacttctcatatatttggcagAGCAAAGATGAAAAATACTTCATCCACAACCATCTATCTTTTACGGTGAAATATCACAGGGATGAGCAAAGGGATGTTTCCAGGATTGTGGCCTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG