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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG

Basic information

species Zea mays
transcript GRMZM2G020976_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 6
gtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagat-cttatacccctcttctggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG--
|||||||| ||||  ||  |||                 | || ||       |  || |||    | |  ||||  || | ||| |    | | |||||| |||| ||||||||||| ||||||||||| ||  |||| || |||||||||||||| |||| | | || |||||||| |||||  |||| | ||||||||||  
gtattattttgatgacctgtttca---------------tattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAGGT

upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g40030.1 (Oryza sativa), 3'ss of exon 6
gtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagat-cttatacccctcttctggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG
|||||||| ||||  ||  |||                 | || ||       |  || |||    | |  ||||  || | ||| |    | | |||||| |||| ||||||||||| ||||||||||| ||  |||| || |||||||||||||| |||| | | || |||||||| |||||  |||| | ||||||||||
gtattattttgatgacctgtttca---------------tattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccagGACTTGTCTGTGGGCCTTCAGTACTTTTTCTGACATATATTCAGGGTGACCTGAAGAAGGCTATAGAATTTCCCTACCTCTATTCCCCTGGGTTTCAG
















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|74233566|gb|DT641480.1|DT641480
EST:     GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG                         GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
genomic: GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
EST: gi|31353270|gb|CD437627.1|CD437627
EST:     GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG                         GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTATATTCAGGGTGACC
genomic: GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
EST: gi|78115508|gb|DV533896.1|DV533896
EST:     GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG                         GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
genomic: GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
EST: gi|71420100|gb|DR805010.1|DR805010
EST:     GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG                         GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
genomic: GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
EST: gi|40303781|gb|CK348168.1|CK348168
EST:     GTGGTGCAATG                         GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
genomic: GTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
EST: gi|71298000|gb|DR784969.1|DR784969
EST:     GTGGGGCAATG                         GT-TTGTTCTGTGG-CCTTTCAGTTCTGTTCTTGACTTACATTCAGGGGGG
genomic: GTGGTGCAATGgtattattct ... tggattacagGTCTTG-TCTGTGGACC-TTCAGTACTGTTCTTGACTTACATTCA-GGGTG
EST: gi|31355902|gb|CD440259.1|CD440259
EST:     GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG                         GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTATATTCAGGGTGACC
genomic: GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
EST: gi|148947455|gb|EC892886.2|EC892886
EST:     GAAAATCTAGTCGCCTTAATAGCTTTGGCCTGATGTGGTACCATG                         GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
genomic: GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
EST: gi|89760089|gb|DY688655.1|DY688655
EST:     GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATG                         GTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC
genomic: GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACC

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: 45 (upstream exon), 49 (downstream exon)
Score: 69

GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 138

GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 313

GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 155

GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct ... tggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG
 tcttaat  putative branch site (score: 155)
                             tcttatacccctcttc  putative PPT
             ttcttatatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacagGTCTTGTCTGTGGACCTTCAGTACTGTTCTTGACTTACATTCAGGGTGACCTAAAGAGGACCATGGAATTTCCATACCTTCATTCTCTTGGGTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA