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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttatacttccatctctcttggcctaacagaaacagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG

Basic information

species Zea mays
transcript GRMZM2G004352_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 9
gtgagttatacttccatct-ctcttggcctaacagaaacagaac------catgtca--tagcctaaa-tgtcggttgatgccgttcttttggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG
||||||| |   |  ||    | |||  |||  ||| ||| | |      ||| ||   ||    | | | |   ||  |     |||| |||| ||  ||||||| ||| | |||||||||||||||||||| |||||||| ||||| || || ||||| || ||||| || ||||| || || ||||| ||||| ||||
gtgagttgtctgtttattaatttttgaactagaagacacaaatcgtgctacatatcgattaatgcagagtttttttttttttgaatcttctggttttgtagGTCCTATTTTCGGCATCACTTCTGAAGAACAATAAAGCAGCTCATGAAGCTCTCATGTCTGCCATGTCGCAGAAGGCCAGTGTCTTGGGCTGCATCGAAG

upper sequence: GRMZM2G004352_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g54640.2 (Oryza sativa), 3'ss of exon 9
gtgagttatacttccatct-ctcttggcctaacagaaacagaac------catgtca--tagcctaaatgtcggttgatgccgt-tcttttggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG
||||||| |   |  ||    | |||  |||  ||| ||| | |      ||| ||   ||    | |  |   ||  |   |  |||| |||| ||  ||||||| ||| | |||||||||||||||||||| |||||||| ||||| || || ||||| || |||                                  
gtgagttgtctgtttattaatttttgaactagaagacacaaatcgtgctacatatcgattaatgcagAGTTTTTTTTTTTTTGAATCTTCTGGTTTTGTAGGTCCTATTTTCGGCATCACTTCTGAAGAACAATAAAGCAGCTCATGAAGCTCTCATGTCTGCCATG----------------------------------
















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|148930743|gb|EC873038.2|EC873038
EST:     CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCA                         GTGAGTCCTGTTTGCTGCATCACTTCT
genomic: CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGT----CCTGTTTGCTGCATCACTTCT
EST: gi|76010525|gb|DT937695.1|DT937695
EST:     CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAATCTTACCAGATGGGCA                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAATCTTACCAGATGGGCA                         GTCCTGTTTGCTGCATCACTTCTGAAGAACA-CAAAGCAGCCCATGAGGCG
genomic: CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|71317337|gb|DR795362.1|DR795362
EST:     CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCA                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|18167877|gb|BM337717.1|BM337717
EST:     CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCA                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     AAGCCCGCA-CTAAGCAAAGATCAGCAACAAAAACTTTAC-AGATGGGCA                         GTCCTGTTTGCTGCATCACTTTCTGA
genomic: AAGCC-GCAACTAAGCAAAGATCAGCAACAAAACCTT-ACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTT-CTGA
EST: gi|149100297|gb|EE186362.2|EE186362
EST:     CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCA                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|148954648|gb|EC900095.2|EC900095
EST:     AAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCA                         GTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: AAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|91872112|gb|EB402069.1|EB402069
EST:     CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCA                         GTCCTGTTTGTTGCATCACTTTTGAAGAACAACAAAGCAGCCCATGAGGCG
genomic: CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCG
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCA                         GTCCTGTTTGCTGCATCACTTCTGAAGA-CAACAAAGCAGCCCA
genomic: CTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCA

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: 47 (upstream exon), 48 (downstream exon)
Score: 10

AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 65

AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG


Block sizes: 14 (upstream exon), 36 (downstream exon)
Score: 1

AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 70

AGGTTCATAAACAGAACTAAGCCGCAACTAAGCAAAGATCAGCAACAAAACCTTACCAGATGGGCAgtgagttata ... ggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG
                                      ttcttttg  CT-rich tract
                   taaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttatacttccatctctcttggcctaacagaaacagaaccatgtcatagcctaaatgtcggttgatgccgttcttttggtatttcagGTCCTGTTTGCTGCATCACTTCTGAAGAACAACAAAGCAGCCCATGAGGCGCTTATGTCAGCGATGTCCCAAAAGGCAAGCGTGTTGGGGTGCATTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG