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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccagagcatttcctgtctttagatctgtattcatgtacacagtttacaggcttcatagtcaattcttttccctgactataaaggaatgcatatc...

Basic information

species Zea mays
transcript GRMZM2G165817_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165817_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 5'ss of exon 2
GCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccagagcatttcctgtctttagatctgtattcatgtacacagtttacaggcttcatagtcaattcttttccctgactataaaggaatgcatatc------
|| |||||||| ||||| ||||| || || |||||||| || ||||| ||||| ||||| || || ||||| || ||||| ||||||||||||||||| |||||||  |||||||||||| | | |     || ||| |  | |     ||       || |  |||   ||        |  | ||     ||| | |       
GCTAAGAAGGACTTTACAAAGACCGAAGATGACTTAAAATCCCTGCAAAGTGTTGGGCAGATCATCGGAGAGGTTCTCCGCCCTCTTGATAATGAACGTTgtaagtaaagagcatttcctttttgtg---ttgaatttacatcctttactttggccactccttatca---ctacagaaaaatcacaagtatttgcttttgccattt
















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|19770216|gb|BQ034937.1|BQ034937
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211243468|gb|FL076790.1|FL076790
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211241231|gb|FL076775.1|FL076775
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|19822398|gb|BQ048422.1|BQ048422
EST:     TGTGGGGCAAATAATTGGATAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|60400478|gb|DN233285.1|DN233285
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211238994|gb|FL076765.1|FL076765
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|22472946|gb|BU037426.1|BU037426
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|15499352|gb|BI595865.1|BI595865
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211239003|gb|FL076774.1|FL076774
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211243473|gb|FL076795.1|FL076795
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211243475|gb|FL076797.1|FL076797
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211243469|gb|FL076791.1|FL076791
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211241239|gb|FL076783.1|FL076783
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211236768|gb|FL076759.1|FL076759
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|148950536|gb|EC896111.2|EC896111
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
EST: gi|211238993|gb|FL076764.1|FL076764
EST:     TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCT                         TTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA
genomic: TGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 537

GCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTAAAGTGGACAAGGAGAAGTTGACATCTGGTACTCGTGTTGTACTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 493

GCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTAAAGTGGACAAGGAGAAGTTGACATCTGGTACTCGTGTTGTACTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 350

GCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTAAAGTGGACAAGGAGAAGTTGACATCTGGTACTCGTGTTGTACTTGACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 453

GCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccag ... gtctcttcagTTATCGTGAAGGCCAGCAGTGGTCCCCGATACGTGGTCGGTTGCCGAAGTAAAGTGGACAAGGAGAAGTTGACATCTGGTACTCGTGTTGTACTTGACAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAGAAGGATTTTACCAAGACTGAGGACGACTTAAAGTCTCTGCAGAGTGTGGGGCAAATAATTGGAGAAGTACTCCGACCTCTTGATAATGAACGCTgtaagtccagagcatttcctgtctttagatctgtattcatgtacacagtttacaggcttcatagtcaattcttttccctgactataaaggaatgcatatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaggaat