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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatttttggccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG

Basic information

species Zea mays
transcript AC233865.1_FGT006
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC233865.1_FGT006 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g19560.1 (Oryza sativa), 3'ss of exon 2
-----------------gtaacatttttg--gccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG
                 |||||||||||   |||||| | |||    | |||||| || |  |  ||     | || |      | | |||| |   | |||||| |  |  | ||| ||||||||||||||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||||||||| |||||||||||||| ||||| ||||
gtatggggtcttcccaggtaacatttttaaagccacttcaaaattactgaagattctttaagccctt---gcttcagtgttgtgataattagtcat-tttctgttctcgatct-caatagAAGGACAAAAGGACTGGGCGTCCAAAAATCTGGATATATAGGGACAAAGTTACCAATGAACCAAAGGGTGATGCGACAGTCACCTATGAAGATCCGCATG

upper sequence: AC233865.1_FGT006 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 2
gtaacatttttg--gccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG
|||||||||||   |||||| | |||    | |||||| || |  |  ||     | || |      | | |||| |   | |||||| |  |  | ||| ||||||||||||||||||||||||||||||| |||||||| |||||||||||||| |||||||||||||||||||| |||||||||||||| ||||| ||||
gtaacatttttaaagccacttcaaaattactgaagattctttaagccctt---gcttcagtgttgtgataattagtcat-tttctgttctcgatct-caatagAAGGACAAAAGGACTGGGCGTCCAAAAATCTGGATATATAGGGACAAAGTTACCAATGAACCAAAGGGTGATGCGACAGTCACCTATGAAGATCCGCATG

upper sequence: AC233865.1_FGT006 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g12800.1 (Oryza sativa), 3'ss of exon 2
----------gtaacatttttggccac-----taccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG
          |   | |    ||| ||     |       |||  |||||| ||||  | |||     | |||||  |    | |||| |   | ||||||||  |  | ||||||||||| |||||||| || ||||||||||| ||||| ||||||||||| ||||| ||||||||||||||||| || |||||||||||||| || |||||||
gtatggatgggggtcttcccaggcaacatttttgtagctgattaaaagattcttcaagcctttgtcgcttcattttcatggtaattagtcat-tttctgttgttgatct-caacagAAGGATAAAAGGACCGGTCGTCCAAAAATCTGGATTTACAGGGACAAGGTTACCAATGAACCAAAGGGTGACGCGACAGTCACCTATGAAGACCCACATG

upper sequence: AC233865.1_FGT006 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------gtaacatttttggccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgta---aaattgca--acagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG
                              |  ||| ||  ||   |   | ||   ||  | ||  | | || |  ||| ||| | |       |  ||   |   | ||| |   |   |  || |     |||| |||||||| || || || || || || ||| | ||| |||||||||| |||||||||||||||||||||||||| || || ||||||||||||||||
gtagttaatctgactggctattatttgaaattccatattgtgcttgttttacaagccttttgttttgtaaaacttgataagttcaaatgctcatccttttcttccattttctttctcattcacgttcctttgtagAAAGACAAAAGAACAGGTCGACCTAAGATATGGTTGTACCGGGACAAAGTCACTAATGAACCAAAGGGTGATGCAACTGTAACATATGAGGATCCACATG

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|211325885|gb|FL059678.1|FL059678
EST:     TGAATATTTTGGCACCATA-GCTTGCCTATAAAGGTATGGGTCTTACCAG                         AAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
genomic: TGAATATTTTGGCACCATAGGCTTG-C--TAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
EST: gi|211328059|gb|FL059693.1|FL059693
EST:     TGAATATTTTGGCACCATAG-CT-GCGTAAAAAGTTATGGNTCTTACCAN                         AANGACAAAANGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
genomic: TGAATATTTTGGCACCATAGGCTTGC-TAAAG-GT-ATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
EST: gi|211328057|gb|FL059691.1|FL059691
EST:     CTGAATATTTTGGCACCATAGTGCTTNNNNNNNGGTATGGGTCTTACCAN                         AAGGACAAAAGGACTGGGGCGTCCAAAAATTTGGATATACAGGGACAAAGT
genomic: CTGAATATTTTGGCACCATAG-GCTT-GCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACT-GGGCGTCCAAAAATTTGGATATACAGGGACAAAGT
EST: gi|211325889|gb|FL059682.1|FL059682
EST:     GCTGAATATTTTGGCACCATAGGCTTGCCTAAAGGTATGGGTCTTACCAG                         AAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
genomic: GCTGAATATTTTGGCACCATAGGCTTGC-TAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
EST: gi|211325891|gb|FL059684.1|FL059684
EST:     CTGAATATTTTGGCACCATAGTGTCCTA-TAAAGGTATGNNTCTTACCAG                         AAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
genomic: CTGAATATTTTGGCACCATAG-G-CTTGCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTT
EST: gi|211325887|gb|FL059680.1|FL059680
EST:     TAAAAAGGTATGGGNNCTTACCANN                         AANGACAAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAG
genomic: TAAA--GGTATGGGT-CTTACCAG-gtaacatttt ... attgcaacagAAGGACAAAA-GGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAG
EST: gi|211325887|gb|FL059680.1|FL059680
EST:     TAAAAAGGTATGGGNNCTTACCANN                         AANGACAAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAG
genomic: TAAA--GGTATGGGT-CTTACCAG-gtaacatttt ... attgcaacagAAGGACAAAA-GGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAG
EST: gi|211044975|gb|FL152243.1|FL152243
EST:     ATATTTTGGCACCATAGTGGCTT-CAAAAAGGGGTATGGGGTCTTACCAG                         AAGGACAAAANGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGT
genomic: ATATTTTGGCACCATAG-G-CTTGCTAAA-GG--TATGGG-TCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAA-GGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGT

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: 46 (upstream exon), 47 (downstream exon)
Score: 72

GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 113

GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 98

GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 76

GGTTCTGTGTATGTCTGCAATCTACCTCCTGGAACTGATGAAAATATGTTGGCTGAATATTTTGGCACCATAGGCTTGCTAAAGGTATGGGTCTTACCAGgtaacatttt ... attgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG
          atttaaagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatttttggccactaccaaaaattttaagattgttcatacattttaaattccatttaaagaacacttagcctcgtctctgttgtaaaattgcaacagAAGGACAAAAGGACTGGGCGTCCAAAAATTTGGATATACAGGGACAAAGTTACTAATGAACCAAAGGGTGATGCAACAGTCACCTATGAGGATCCACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT