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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtttcatagattttggttgctaccccccctaactcgattttggaggtcttttatctttcgggtttcgattcatccgttttgcagcacagccgg...

Basic information

species Zea mays
transcript GRMZM5G800112_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G800112_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtttcatagattttggttgctaccccccctaactcgattttggaggtcttttatctttcgggtttcgat-tcatccgttttgcagcacagccgg------
|| |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||| |||| || |||||||| |||||||||||||||  ||  |       | |       | |||||| |  || |  || |   | | |  |    ||||  ||||  | || |    |||| | |  ||  |       
GTGGTGCGGAAGAAGGCGCCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCCCGCCGCTCCGGCGCCGAGATCGAGACCATGAAGAAGTgtgcgtact-------actgcctcccccaccccctcctacccttttcttttgatttgattcgattcgcttttccctctccttttctttgaatcgaaggggttctttt

upper sequence: GRMZM5G800112_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G42900.1 (Glycine max), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtttcatagattttggttgctaccccccctaactcgattttggaggtcttttatcttt-----cgggtttcgattcatccgttttgcagcacagccgg-
||  | || |||||||| ||||| ||||||||||||||||||||||| |||||||||||||| |||||| |||| || || ||||| ||| | || || |||   |  || |  | |   |    | |    |   | | |   ||||     |||||| | |||       || |  ||       ||||    | |     |  
GTCCTCCGCAAGAAGGCTCCCACTGCCGCCGCCAAGAAGGATGAGAAAGCCGTCAACGCCGCCCGCCGCTCCGGCGCCGAAATCGAAACCCTAAAAAAATgt---tccttcccaaaaccctcaccgattgatcaatttattgtcttttct---tcttttgtttttaaatataggatctgaacttcttgtttcttgggattattgca

upper sequence: GRMZM5G800112_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G42890.1 (Glycine max), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtttcatagattttggttgctaccccccctaactcgattttggaggtcttttatctttcgggtttcgatt--catccgttttgcagcacagccgg-
||  | || |||||||| ||||||||||||||||||||||| ||||| |||||||||||||| |||||| | || || || ||||| ||| | || ||||||   | ||| | || |   |  ||   |       |||    |  |    |     || |   ||| || | ||||  | | |  ||   ||      |   
GTCCTCCGCAAGAAGGCTCCCACCGCCGCCGCCAAGAAGGACGAGAAAGCCGTCAACGCCGCCCGCCGCTCTGGCGCCGAAATCGAAACCCTAAAAAAGTgt---tcgttccctaaaccctcattcaaaaaaatagtaatagtaaatcttcgaatagttgttcgtcgcgtgttgattgtcttacaattataagtttcttctaa

upper sequence: GRMZM5G800112_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G15420.1 (Glycine max), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtttcatagattttggttgctacccccccta-actcgattttggaggtcttttatctttcgggtttcgattcatccgttttgcagcacagccgg-----
||  | || |||||||| ||||||||||||||||||||||| ||||| |||||||||||||| || ||| |||| ||||| || || ||| | || ||||||   | ||| |  | |   |  | |  |     | || | |  || || ||      || |   ||| || | |||| ||| |      |  |    |       
GTCCTCCGCAAGAAGGCTCCCACCGCCGCCGCCAAGAAGGACGAGAAAGCCGTCAACGCCGCCCGGCGCTCCGGCGCGGAAATTGAAACCCTAAAAAAGTgt---tcgttcccaaaaccctcatcgaaaaaaaacatataataaatattcgaa--tagttgttcgtcgcgtgttgatt-atctgacaaatataaatttcttctcac

upper sequence: GRMZM5G800112_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G15410.1 (Glycine max), 5'ss of exon 1
------------------------------GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtttcatagattttggttgctaccccccctaactcg--attttggaggtcttttatctttcgggtttcgattcatccgttttgcagcacagccgg
                              ||  | || |||||||| |||||||| ||||| |||||||| ||||| |||||||||||||| |   || | ||   | | ||| | ||| | || |||| |   | ||| |  | |   |  | |       |  | | | |   | ||   |                                                
GGCCCTCTTTCTCTGGATTGGGAACCCGTCGTCCTCCGCAAGAAGGCTCCCACCGCTGCCGCTAAGAAGGACGAGAAAGCCgtcaacgccgcccaatgctctggcttg-aaatcaaaaccctaaaaaagtat---ttgttgccaaaaccctaatcgaattgatcagttaattgttgtcttcacga-----------------------------------------------

upper sequence: GRMZM5G800112_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv19s0014g01260.t01 (Vitis vinifera), 5'ss of exon 1
GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtttcatagattttggttgctaccccccctaactcgatttt----ggaggtcttttatctttcgggtttcgattcatccgttttgcagcacagccgg
||  | ||||||||| | | || |||||||||||||||||| ||||| |||||||||||||| || |||   || || |||||||| ||  | ||||||||||      ||  |   |||   |  | |       |   |   ||||     ||  |||||      | |  |    ||  |    | ||         ||  
GTGATCCGGAAGAAGCCTCTCAACGCCGCCGCCAAGAAGGACGAGAAAGCCGTCAACGCCGCCCGTCGCATGGGCGCCGAGATCGAGACTGTCAAGAAGTgtattcccctttctc--tttctttccccattttttttcgttgtttttttcgaagaaatctttggagggtagaatgagaatcgaaaaatattttttattttcc--

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|211137933|gb|FL090170.1|FL090170
EST:     CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
EST: gi|211137002|gb|FL090161.1|FL090161
EST:     CGTCAACGCCGCGCGCCGCG-CGGTGCGGAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
EST: gi|15005220|gb|BI325287.1|BI325287
EST:     CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATC
genomic: CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATC
EST: gi|211137930|gb|FL090167.1|FL090167
EST:     GTCAACGCCGCGCGCCGS-C-GGTTGCGAAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: GTCAACGCCGCGCGCCGCGCCGGT-GCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
EST: gi|211137007|gb|FL090166.1|FL090166
EST:     CGTCAACGCCGCGCGCCGSSC-GGTGCGAAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
EST: gi|101399867|gb|EB821780.1|EB821780
EST:     GATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: GATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
EST: gi|211142486|gb|FL118083.1|FL118083
EST:     GTCAACGCCGCGCG-C-CGSCGGTTGCGGAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: GTCAACGCCGCGCGCCGCGCCGG-TGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
EST: gi|211136052|gb|FL090147.1|FL090147
EST:     CGTCAACGCCGCGCGCCGCG-CGGTGCGGAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
EST: gi|15208834|gb|BI430718.1|BI430718
EST:     CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
EST: gi|22473062|gb|BU037542.1|BU037542
EST:     CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAG
genomic: CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAG
EST: gi|211137931|gb|FL090168.1|FL090168
EST:     CGTCAACGCCGCGCGCCGSSC-GGTGCGTAGATCGATACCATGAAGAAGT                         ACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA
genomic: CGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCA

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 2 RNA-Seq libraries.


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 100

GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 63

GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtt ... ttttctgcagACAACGCTGGTACGAACAAGGCGGCATCCAGCGGTACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTGCGGAAGAAGGCACCCACCGCCGCCGCCAAGAAGGATGAGAAGGCCGTCAACGCCGCGCGCCGCGCCGGTGCGGAGATCGATACCATGAAGAAGTgtaagtggtttcatagattttggttgctaccccccctaactcgattttggaggtcttttatctttcgggtttcgattcatccgttttgcagcacagccgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc