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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattattattttcatgcattggaccttaataacttcttctgatgctatatggttacgtctttgttcccccctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG

Basic information

species Zea mays
transcript GRMZM2G133885_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133885_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 17
-gtattattattattttcatgcattggaccttaataacttcttctgatgctatatggttacgtctttgttcccccctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
  | |  |||    |||  ||  |    |   |       |   ||   | | |   |  |   |   |       ||| ||||||||| |||||| | ||||||||||| ||||| ||||||||||| ||||||
gttttctttacgcatttgttgtttcatgcaacagctgtaccgcttgtgtccacagattatctaatgcatgatattttctcccagTTTGGATATTTCGCTTTTGGAGGGAGCACAGTAATATGCGTCTTTGAGAAG
















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|5922429|gb|AW055718.1|AW055718
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGCCCAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|32844513|gb|CD984194.1|CD984194
EST:     GCATCACGTTCTTGAAAAAAGATGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGT
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGT
EST: gi|6194556|gb|AW146660.1|AW146660
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCATAGGAGAAGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTTGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|6021540|gb|AW066468.1|AW066468
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGCACAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|37361294|gb|CF602583.1|CF602583
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|32912653|gb|CF017465.1|CF017465
EST:     GCATCACGTTCTTGAAAAAAGATGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|33770671|gb|CF272965.1|CF272965
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|6095730|gb|AW120397.1|AW120397
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGG
EST: gi|32913231|gb|CF018043.1|CF018043
EST:     GCATCACGTTCTTGAAAAAAGATGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|211196234|gb|FL472452.1|FL472452
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|60396723|gb|DN229588.1|DN229588
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|78103985|gb|DV522403.1|DV522403
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTTTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
EST: gi|40302877|gb|CK347264.1|CK347264
EST:     GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG                         TTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
genomic: GCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG

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: 79

GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 63

GTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAGgtattattat ... cctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaataacttcttctgatgctatatggttacgtctttgttcccccctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG
                            ttacgtctttgttccc  CT-rich tract
                     tatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattattattttcatgcattggaccttaataacttcttctgatgctatatggttacgtctttgttcccccctcttccagTTTGGGTATTTCTCCTTTGGAGGGAGTACAGTGATATGCGTCTTCGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG