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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtattaattcagtgccaagtttcttttaaccttgcctgtttaaatctatctgcatgatattggtgtacactatattacagaattcggtgtgcttat...

Basic information

species Zea mays
transcript GRMZM2G140917_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 14
AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagta-ttaatt-cagtgccaagtttcttttaacct----tgcctgtttaaatctatctgcatgatattggtgtacactatattacagaattcggtgtgcttat
|||||||||| || |||||||||||||||||||| ||||| ||||| |||||||| ||||||||||||||||| ||||| ||||||||||| ||||||||||||||  |||||  || |||||||||| ||||  | |    |||  || ||||| | | |||| |   | |   |||| || |||| |  |       |      
AGTATGATCCACGTCCTGTTCAACCTGATTCTCTCTTTCCAGTTTTTTCAGTGACAAAGGGTATCACTGCTGGCATGGTGCATTGGCTTGTTGACAAAGGgtgagtgcttaatcacaatgccaagttttttttttcttaacatgctagtgtaaatatgtttgcaggccgtcgtattacagtacattatactacctcagat------

upper sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 16
lower sequence: GLYMA17G24440.1 (Glycine max), 5'ss of exon 1
AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtattaattcagtgccaagtttcttttaaccttgcctgtttaaatctatctgcatgatat-tggtgtacactatat-tacagaattcggtgtgcttat-
| |||||||| || || ||||| ||||||   ||||||||||| ||||| || || ||||||||||| || || ||| |||||||||| || ||||| ||||  ||  |||     ||| | |    | |  |   | |     | ||    |     | || | | || |     | || |  ||  |||  |   | ||  
AATATGATCCACGTCCGGTTCAGCCTGATAGCCTTTTTCCTGTGTTCTCTGTTACGAAGGGTATCACAGCAGGAATGATACATTGGCTGGTTGACAATGGgtatgttgtaac---atgctatgaccatatagattgtacgccccttaactggttgctgtaatttcttgtttgtcggacatgtggagttttcatttgacataga

upper sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 16
lower sequence: AT5G24810.2 (Arabidopsis thaliana), 5'ss of exon 15
AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtattaattcagtgccaagtttcttttaaccttgcctgtttaaatctatctgcatgatattg-gtgtacactatattacagaat-tcggtgtgcttat--------------------------------------------------------------------
  ||||| || || || |||||||| |||  | | |||||||||||||| ||||| |||||| |||||||||| ||| ||||||||||||| |||||| ||||||||  ||  || |   |  ||||    ||  |    | || |  ||   |  | |||||||  |  |   ||  | |     || | ||| |  || |                                                                    
GATATGACCCTCGTCCAGTTCAACCCGATAGTTTATTTCCTGTTTTCTCTGTGACAAAGGGTGTCACTGCTGGAATGATACATTGGCTTGTTGACAAAAGgtgagtaacaa--cattttaagctttcaaaaaatttcatgtattcatttcacacaccctgatattttgaatcggctccaatcttacatattggtctcattgttaattccatgatcccatttgcagaacacatgcttagtcatatttagtaatatttattcaatgatacag

upper sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 16
lower sequence: Vv04s0008g02740.t01 (Vitis vinifera), 5'ss of exon 14
AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtattaattcagtgccaagtttcttttaaccttgcctgtt--taaatctatc---tgca-tgatattggtgtacactatattacagaattcggtgtg-cttat
  |||||||| || || ||||||||||||   || |||||||||||||| || || |||||||| || || || ||| |||||||||| || ||||||||||  ||   ||||  |||   | |  || ||||  |||| ||||  | |||| ||    |||| |    ||  | | |||     | | |    |    || |  | 
GATATGATCCTCGTCCAGTTCAACCTGATAGCCTATTTCCTGTTTTCTCCGTAACAAAGGGTATTACAGCAGGAATGATACATTGGCTGGTTGACAAAGGgtatgt---aatt--gtgatta-tgactattaatgttgcatgttcttgaatccattcagtgcaattgcgttcctttccacctccatcctgccaccaacatggcaca-

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|211402617|gb|FL252145.1|FL252145
EST:     GTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGG                         GAAGCTGAAGTACGAGGAAACAGTTGCCAACATATGGCCGAATTTTGGAAC
genomic: GTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtatta ... aatctttcagGAAGCTGAAGTACGAGGAAACAGTTGCCAACATATGGCCGAATTTTGGAAC
EST: gi|148966697|gb|EE017760.2|EE017760
EST:     GTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGG                         GAAGCTGAAGTACGAG
genomic: GTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtatta ... aatctttcagGAAGCTGAAGTACGAG
EST: gi|67017334|gb|CO446083.1|CO446083
EST:     GTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGG                         GAAGCTGAAGTATGAGGAAACAGTTGCCAACATATGGCCGAATTTTGGAAC
genomic: GTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtatta ... aatctttcagGAAGCTGAAGTACGAGGAAACAGTTGCCAACATATGGCCGAATTTTGGAAC

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: 38

AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtatta ... aatctttcagGAAGCTGAAGTACGAGGAAACAGTTGCCAACATATGGCCGAATTTTGGAACTAACGGAAAGGAGTTAATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtatta ... aatctttcagGAAGCTGAAGTACGAGGAAACAGTTGCCAACATATGGCCGAATTTTGGAACTAACGGAAAGGAGTTAATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtatta ... aatctttcagGAAGCTGAAGTACGAGGAAACAGTTGCCAACATATGGCCGAATTTTGGAACTAACGGAAAGGAGTTAATAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

AGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTGTTTTCTCAGTGACTAAGGGTATCACTGCTGGGATGGTACATTGGCTTGTGGACAAAGGgtgagtatta ... aatctttcagGAAGCTGAAGTACGAGGAAACAGTTGCCAACATATGGCCGAATTTTGGAACTAACGGAAAGGAGTTAATAAAG