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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcatattgttctgttaatcagtttaaatggccttgtatttgtgtcaaattttcattgcttgtctgtacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG

Basic information

species Zea mays
transcript GRMZM5G811223_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 19
gttcatattg---------ttctgttaatcagtttaaatggccttgtatttgtgtcaa-attttcattgcttgt----ctgtacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
||| | |||          |    ||  ||| || |   | || |||  ||||| |||  || | |||| || |    ||   ||| | ||||||||||| |||||||||||||||| ||||||||||| ||||| ||||||||||| || || |||||
gtttacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcagGCTATTGTGTTGTGCCAAGTGGAGAAGGCAAAGGAAGATATGCTAAACCAGCTATATAGTTCAATAAG

upper sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 19
gttcatattgttctgttaatcagtttaaatggccttgt---atttgtgtcaaattttca--ttgcttgtctgt-acttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
  | |  || || | | ||  |   ||  |   ||  |   |||||   |   || | |  |   ||  || | |||    ||||  |||| || |||||||| |||||||| || ||||||||||| |||||||||||||| || || ||
-gtgagtttattttatcaactaccatagttcttctcttctgatttgacgcggtttgtgagatgatttcactttgactgagcagGCAGTTGTTCTTTGCCAAGTAGAGAAAGCCAAAGAAGACATGCTCAACCAGCTATACAGTTCCATCAG

upper sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 19
gttcatattgttctgttaatcagtttaaatggccttgt---atttgtgtcaaattttca--ttgcttgtctgtacttgt-tagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
  | |  || || | | ||  |   ||  |   ||  |   |||||       || | |  |   ||  || |  |||   ||||  |||| || |||||||| |||||||| || ||||||||||| |||||||||||||| ||  | ||
-gtgagtttattttatcaactaccatagttcttctcttctgatttgatgtggtttgtgagatcatttcactttggttgagcagGCAGTTGTTCTTTGCCAAGTAGAGAAAGCCAAAGAAGACATGCTGAACCAGCTATACAGTTCCGTCAG

upper sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 19
------------------------------gttcatattgttctgttaatcagtttaaatggccttgtatttgt--gtcaaattttcat----tgcttgtctgtacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
                               |  | ||| |  |||  |||  |||       |    |||  |  ||||   |   |     ||    |      |    ||||| |||| || || ||||| ||||||||||||||||||||||| || || || ||||| || |||||
gtgaactatccttatgcaaaagctcgaaagctctaaattttcttgtccatctcttttctcttacagagattcctcggtcatgctactaagcgatgtgaattgaccatgaacagGCTGTTGTTCTTTGTCAAGTAGAGAAAGCAAAGGAAGACATGCTGAATCAACTCTACAGTTCTATAAG

upper sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 19
--------gttcatattgttctg--ttaatcagtttaaatggccttgta----tttgtgtcaaattttcattgcttg-tctgta--cttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
        ||   | || || ||  ||  | | ||   ||| |  | |     ||  |  |    |  |||| ||   |||||    |    ||||| |||| || || |||||||||||| | |||||||||||||| || |||||||||||||| || ||
gtggactagtcacttttcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacagGCTGTTGTTCTCTGTCAAGTGGAGAAATCCAAGGAAGACATGCTGAATCAGCTATACAGCTCTATCAG

upper sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 19
gttcatattgttctgttaatca--gtttaaatggccttgtatttg-----tgtcaaat-tttcattgcttgtctg--tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
||    | |  ||  | |||     |||      | ||  || ||     |  |||||  || | |   ||   |  |  |||  ||||  |||| || |||||||| |||||||| |||||||||||||| || ||| | |||||||| || ||
gtaagcacttgtccctgaattctcatttttgcatctttacatctggtcacttacaaatgcttgaatatgtgatcgattggttggcagGCAGTTGTTCTTTGCCAAGTTGAGAAAGCTAAGGAAGACATGCTAAATCAGTTGTACAGCTCAATCAG

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|211235185|gb|FL451892.1|FL451892
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAG                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211346182|gb|FK944396.1|FK944396
EST:     TTTGAATAGTCTGGCAGCAAATGTTCCGAA-                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: TTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211348570|gb|FK944397.1|FK944397
EST:     TTTGAATAGTCTGGCAGCAAATGTTCCGAA-                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: TTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|32937777|gb|CF042596.1|CF042596
EST:     GTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAAG                         GCTATTGTGCTTTGTCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211235186|gb|FL451893.1|FL451893
EST:     AATAGTCTGGCAGCAAATGTTCCGAAG                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: AATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|31348909|gb|CD433266.1|CD433266
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAG                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211346179|gb|FK944393.1|FK944393
EST:     TTTGAATAGTCTGGCAGCAAATGTTCCGAA-                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: TTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211346181|gb|FK944395.1|FK944395
EST:     TTTGAATAGTCTGGCAGCAAATGTTCCGAA-                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: TTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211348571|gb|FK944398.1|FK944398
EST:     TTTGAATAGTCTGGCAGCAAATGTTCCGAA-                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: TTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211346180|gb|FK944394.1|FK944394
EST:     TTTGAATAGTCTGGCAGCAAATGTTCCGAA-                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: TTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211348572|gb|FK944399.1|FK944399
EST:     TTTGAATAGTCTGGCAGCAAATGTTCCGAA-                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: TTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|211132354|gb|FK982421.1|FK982421
EST:     GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAG                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
EST: gi|67010855|gb|CO439604.1|CO439604
EST:     GTGGTTATGTTGAGGCTGTTTTGAATATTCTGGCAGCAAATGTTCCGAAG                         GCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG
genomic: GTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAG

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), 49 (downstream exon)
Score: 224

GAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

GAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 273

GAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 188

GAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattg ... tacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaaatggccttgtatttgtgtcaaattttcattgcttgtctgtacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG
                         aaattttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcatattgttctgttaatcagtttaaatggccttgtatttgtgtcaaattttcattgcttgtctgtacttgttagGCTATTGTGCTGTGCCAAGTGGAGAAAGCAAAGGAAGACATGCTTAACCAGCTATACAGCTCGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC