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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatttctttgttgttacatttggcacctgctgagcagggcactcattatgttaatttgtattactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGTTTGGTCAAAAGTGTAGCGTTATTGATGGTTTTGGCTGCTCTGGTCCCTG

Basic information

species Zea mays
transcript GRMZM2G453794_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g02756.2 (Oryza sativa), 3'ss of exon 15
gtaatatatttctttgttgttacatttggcacctgctgagcagggcac-tcattatgttaatttgt------------attactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGTTTGGTCAAAAGTGTAGCGTTATTGATGGTTTTGGCTGCTCTGGTCCCTG
|||    | ||| || ||  |  ||  || | |||   |  |   ||  ||   || |||| ||||            |||| | ||||||| || ||||| || |||||||| ||||| |||||||| |||||||| ||  |  |||||||  | ||| || ||||||||||||| |   ||||    |
gtatgtgaattccttattactgtatgaggtatctgagtaatatcacatatctggatattaacttgttttctttattgtattaatctgcagGTATTCGGTTTGAATCCCAAGGCGATGGTGCATTTCCAGTTGTTCCTCCGACTTATCAAAAGCATTGCGCTACTGATGGTTTTGGCGGGCTTGGTTGTGG
















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|9732693|gb|BE511445.1|BE511445
EST:     TGGGCTG-GCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|22545826|gb|BU098200.1|BU098200
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|67031292|gb|CO460041.1|CO460041
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAA-CCCCA-GGCCATGGTACATTTCCAAT-GTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|84980995|gb|DW531344.1|DW531344
EST:     TTGGTGGCCTTTTC-TCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|60397477|gb|DN230293.1|DN230293
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|50322941|gb|CO518067.1|CO518067
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCG
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCC-AAGGCCATGGTACATTTCCAATTGTTCCTGCG
EST: gi|6578074|gb|AW244211.1|AW244211
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|67015741|gb|CO444490.1|CO444490
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|211408841|gb|FL082351.1|FL082351
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|211406286|gb|FL082346.1|FL082346
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|78120961|gb|DV539345.1|DV539345
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|6194536|gb|AW146640.1|AW146640
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|67040750|gb|CO467005.1|CO467005
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|60357590|gb|DN224563.1|DN224563
EST:     GTATTGGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: GTATT-GGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
EST: gi|26558188|gb|CA830423.1|CA830423
EST:     TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTG                         GTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT
genomic: TGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGT

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: 359

GTGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGTTTGGTCAAAAGTGTAGCGTTATTGATGGTTTTGGCTGCTCTGGTCCCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 163

GTGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGTTTGGTCAAAAGTGTAGCGTTATTGATGGTTTTGGCTGCTCTGGTCCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

GTGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGTTTGGTCAAAAGTGTAGCGTTATTGATGGTTTTGGCTGCTCTGGTCCCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 213

GTGTATTGGATTTCTTGGGCTGTGCTTGGTGGCCTTTTCATCCTCCTCTTGgtaatatatt ... tactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGTTTGGTCAAAAGTGTAGCGTTATTGATGGTTTTGGCTGCTCTGGTCCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttggcacctgctgagcagggcactcattatgttaatttgtattactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGTTTGGTCAAAAGTGTAGCGTTATTGATGGTTTTGGCTGCTCTGGTCCCTG
                                tgttaat  putative branch site (score: 213)
                            attatgttaatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatatttctttgttgttacatttggcacctgctgagcagggcactcattatgttaatttgtattactatgcagGTCTTTGGTTTAAACCCCAAGGCCATGGTACATTTCCAATTGTTCCTGCGTTTGGTCAAAAGTGTAGCGTTATTGATGGTTTTGGCTGCTCTGGTCCCTG

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