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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgggatattttcttcaattgcattagcaaattccagtctctgtgactataactgcaacctaaaaccaattctcttttgccttttgtcacggctatgaattgtgccaggtggaattaatgttgtctttgtctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAAC

Basic information

species Zea mays
transcript GRMZM2G073571_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073571_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 11
gttagtgggatattttcttcaattgcattagcaaattccagtctctgtgactataactgcaacctaaaaccaattctcttttgccttttgtcacggctatgaattgtgccaggtggaattaatgttgtctttgtctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGA-GCAAC
                            |      || ||  ||||     |||   | |||  ||||  |  ||||| |||    | ||| |    |||| ||| |||||  |  ||||||     || ||  ||   | ||||||| ||||| || || || ||||||||||||||  | |||||||| ||||| ||||| || || ||||| || ||||| |||||||||||||| |  | 
----------------------------tgctggcttgcatcctct-----tatg-ttacaaaataaatgct-ttctcctttaagctctgttat---tatggattatgccactta-aattaa----atcatttccttcttcagGTCAAGATGGTTAGAGCCACGAGCTTTTCTACTCGCATGCCTGAATACGATGTTCCTGTCGTCGATAAGGCTGTAGATGCAACATGGAAGAGAGAAGTGA-
















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|8383108|gb|BE055991.1|BE055991
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|15177587|gb|BI398526.1|BI398526
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTCGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|16137338|gb|BI894203.1|BI894203
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTCGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|3172014|gb|AJ006545.1|AJ006545
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|15177586|gb|BI398525.1|BI398525
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTCGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|15188204|gb|BI417181.1|BI417181
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTCGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|15323597|gb|BI478855.1|BI478855
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTCGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|15323596|gb|BI478854.1|BI478854
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTCGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|32832349|gb|CD972027.1|CD972027
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTCTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT
EST: gi|32847771|gb|CD987452.1|CD987452
EST:     CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAG                         GTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTCTCCCTGAATATGAT
genomic: CTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGAT

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), 46 (downstream exon)
Score: 162

ATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAAC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 77

ATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAAC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 81

ATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 110

ATCAACTGCTGAGTCTGGTTCAGAAGCTGATGATGCTGTGTCCCCCAAAGCTCTCAGAAGTTACATATCACATCCTAAGTTGACCCCAGTTCGTGAAGAGgttagtggga ... tctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcacggctatgaattgtgccaggtggaattaatgttgtctttgtctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAAC
                            aattaat  putative branch site (score: 110)
                                    ttgtctttgtctct  CT-rich tract
                            aattaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgggatattttcttcaattgcattagcaaattccagtctctgtgactataactgcaacctaaaaccaattctcttttgccttttgtcacggctatgaattgtgccaggtggaattaatgttgtctttgtctctattagGTCAAAATGGTCAGGGCTACTAGCTTTTCTACTCGTGTCCCTGAATATGATGTACCTGTTGTTGACAAGGCCGTGGATGCTACATGGAAGAGAGAGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA