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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggtctactgataagtgcacattttgattgtttccttgtttttgctcttttctgcattgttctgtttcaacttattggctgatttaaatgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA

Basic information

species Zea mays
transcript GRMZM2G416120_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 6
--------------------------tgtggtcta-ctgataagtgcacattttgattgtttccttgtttttgctct---tttctgc-attgttctg--tttcaacttattggctgatttaaatgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA
                            ||| ||  || ||   |      || |     ||||||   ||    ||    || ||| |    ||||  |||    | ||| | |   |||||  ||  ||||||||| ||||||||||| |||||||||||||||||||| || ||||||||||||||||| ||||||||||| |||||  |||||||| ||||  ||||||
gtaagttgatccaagttaaaactgaacttggcctctcttatctctatttggttggtagacttcctttagttaaaactgaacttgtgccaacactctggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA

upper sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtggtctactgataagtgcacattttgattgtttccttgtttttgctcttttctgcattgttctgtttcaacttattggctgatttaaatgttc-tgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA
                  |    ||    ||  | |||   | |     | || ||| || |||   || |  | |         | |  | ||  |  |||||||||| ||| | | ||||||||| |||||||| |||||||||||  ||||||| || |||||||| ||||||||||| || ||| | ||| | || |
------------------gtgagttgaattttatccctaaatgtcaaattattttgc-ttattcc--ttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA

upper sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 6
-tgtggtctactgataagt-gcacattttgattgtttccttgtttttgctcttttc-tgcattgttctgtttcaacttattggctgatttaaatgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA
 ||   |    |   || | |  |||| |     |     | |  | | |   |   ||||   |  || | |  | |  |||  | || |  |    || |||| || || || || | ||||||| | || ||||||||||||||||| || |||||||| || |||||||| || ||||| ||||| || ||  | || |
ttgaaataagataccaatttgtgcattatacgcctcaggatatgatagataagtgaatgcaacctagtgctcc--cgtgatggacggtt-acgttccttgcagGACGGAAAAACTCTGTTTAATGAGTTGGAGGTTGTGGAGGGTATGAAGCTCGACAGAGGATATATCTCTCCCTATTTCATCACCAATTCTAAGACTCAAA

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|71425566|gb|DR806758.1|DR806758
EST:     GTGTGATCACTATTGCA                         GATGGCAACACCCTTTATAATGAGC-TGAAAGTTGTGGAGGGTATGAAACT
genomic: GTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTG-AAGTTGTGGAGGGTATGAAACT
EST: gi|91054374|gb|EB164792.1|EB164792
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAACACCCTTTATAATGAGCTTGAAAGT-GTGGAGGGTATGAAACT
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAA-GTTGTGGAGGGTATGAAACT
EST: gi|71758555|gb|DR956492.1|DR956492
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
EST: gi|149073906|gb|EE162234.2|EE162234
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
EST: gi|78078492|gb|DV506905.1|DV506905
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
EST: gi|67019174|gb|CO447923.1|CO447923
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCT                         GATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
EST: gi|166423857|gb|EG055810.1|EG055810
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAACACCCTTTATAA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAA
EST: gi|149077207|gb|EE165873.2|EE165873
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
EST: gi|32929704|gb|CF034516.1|CF034516
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
EST: gi|166697073|gb|EG200835.1|EG200835
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAAACACCCTTTATAA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAA-CACCCTTTATAA
EST: gi|71425565|gb|DR806757.1|DR806757
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCG                         GATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTT

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), 48 (downstream exon)
Score: 680

GTGGGTACAATATCAGCAAATGGAGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 265

GTGGGTACAATATCAGCAAATGGAGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 531

GTGGGTACAATATCAGCAAATGGAGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 645

GTGGGTACAATATCAGCAAATGGAGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTGATCACTATTGCGgtaagttaaa ... tgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcttttctgcattgttctgtttcaacttattggctgatttaaatgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA
                                 ggctgat  putative branch site (score: 645)
                                      atttaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtggtctactgataagtgcacattttgattgtttccttgtttttgctcttttctgcattgttctgtttcaacttattggctgatttaaatgttctgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA

- - -tctactg
- - - - - - - - - gcacatt
- - - - - - - - - - - - -ttgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggctgat