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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacag

Basic information

species Zea mays
transcript GRMZM2G020976_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 5'ss of exon 6
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagatct-tatacccctcttctggattacag
||||||||||||| || |||||||| ||||||||||||||||| ||||||||| ||||  ||  |||                 | || ||       |  || |||    | |  ||||  ||   ||| |    | | |||||| |||
GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACGgtattattttgatgacctgtttca---------------tattcataatatccagattaaaccatatttgccttagcattcatatcctatccatttggattccag

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G32030.1 (Glycine max), 5'ss of exon 6
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattctgattgcccttttttcttctcgaacac-tgttttttattgctcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacag
| ||| ||||||| ||||||||||||||||| ||||||||||||||||   || |||||    |  |  | | |  |||      |||||||||      |    || |||||||   || | ||     ||   |||  |  |||| ||
GGAAAACTAGTGGTCTTAATAGCTTTGGCCTAATGTGGTGCAATGgtaagcttatgatttgtataatggcctgttaaacttaccctttttattgt-----aacgaaatttcttat---ttgaaat-----acttttctattttattatag

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA14G14360.1 (Glycine max), 5'ss of exon 6
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacag
| ||| ||||||| ||||||||||||||||| ||||||||||||||||   || |   |       |  | | |  |||    ||| |||   || || |||  |||    ||| |  |  ||    ||||   |||  |  |||| ||
GGAAAACTAGTGGTCTTAATAGCTTTGGCCTAATGTGGTGCAATGgtaagcttatatattgtacaatggcctgttaaac----tttcttacc-ctttttattgtaacagaatatcttatttgaa---atacttttctattttattatag

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G07030.1 (Glycine max), 5'ss of exon 6
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct-gattgc-ccttttttcttctcgaacactgttttttattgct---------cttaatttcaacttcttatatcttaa----gatcttata---cccctcttctggattacag
| ||| ||||||||||||||||||||||||| |||||||| |||||||   |  | |||||   |   |  | | ||      | |||||| ||| |         | |  ||     |  || ||   |||    ||| | | |       |||  |   ||| ||
GCAAAACTAGTGGCCTTAATAGCTTTGGCCTTATGTGGTGTAATGgtaagctgatagattgtatcaaatggcctatcagttgtttttttttcttggtaaaagaaagcatgcttgtttttctttttaatctaattgtgatttgaaagaatttttctattatgttatag

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA06G07120.1 (Glycine max), 5'ss of exon 4
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattct-gattgc-ccttttttcttctcgaacactgttttttattgct------cttaatttcaacttcttatatcttaagatcttat------acccctcttctggattacag
| ||| ||||||||||||||||||||||||| ||||||||||||||||   |  | |||||   |   |  | | || |||  | ||||||  |         | |  ||      | ||  |||| ||  |  |||      |    | |  ||  ||| ||
GCAAAACTAGTGGCCTTAATAGCTTTGGCCTTATGTGGTGCAATGgtaagctgatagattgtatcaaatggcctatcaaactttttttttttgtaaaagaaagcatgcttgttttctttttaatctaaatgtggtatgaaataatttttttattgtgttatag

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT4G32272.2 (Arabidopsis thaliana), 5'ss of exon 7
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacag
| ||||| |||||| | |||||||||||||| ||||||| |||||||| |||    | |   |   |  ||      || ||      |      |||  ||| || || | | || || | ||  ||                     
GTAAATCAAGTGGCTTGAATAGCTTTGGCCTTATGTGGTCCAATGgtaatata--aactaaacagataactaaattgaccctaaacact-caagacttgctttgaatttgtgagattttca-atgatag--------------------

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv11s0016g05710.t01 (Vitis vinifera), 5'ss of exon 6
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgtattattctgattgcccttttttcttctcgaacactgttttttattgctcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacag
||||||| |||||||| | |||||||||||| |||||| |||||||||  ||  |   |  |               |     ||||| | | || || |    ||     || ||      || ||       |    |   | ||||
GAAAATCCAGTGGCCTCAGTAGCTTTGGCCTTATGTGGAGCAATGgtaagatgataggtttcaaacagagacagattaattgatttttaaatccttttgaa--aaaagaaataaattggggcatatttgtttaattgaatttttcacag

upper sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv04s0008g05570.t01 (Vitis vinifera), 5'ss of exon 6
GAAAATCTAGTGGCCTTAATAGCTTTGGCCTGATGTGGTGCAATGgta---tta----ttctgattgcccttttttcttctcgaacactgttt-tttattgctcttaatttcaacttcttatatcttaagatcttatacccctcttctggattacag----------------------------
| ||||||||||||||||||||||||||||| |||||||| |||||||   |||    |||  | |||   | || |||     |  ||| || |||  |   |  |||| |    |    | | ||   ||  ||||||  |       ||   |                             
GGAAATCTAGTGGCCTTAATAGCTTTGGCCTAATGTGGTGTAATGgtaagcttaaaaattccaactgcttgtattcctttagacatgctgattattttcttggcagaattacttaatggggtttatttgaatgctataccttttcagaaaatcttattacatcttttttttttctttttttatag

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