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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctctagcccttaccctctcacacatttgtgtggtatctattattctaacacatgtttgttgcag

Basic information

species Zea mays
transcript GRMZM2G097226_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 12
CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctctagccct---taccctctcacacatttgtgtg-----gtatctattattctaacacatgtttg--ttgcag
|||||||||||||| |||| ||||||||||| || ||||| ||  ||||||||||  |||| ||| | ||||| || |||||||||||||| |||||||||| | ||||  | |    | |  |  ||||| | ||||||     | |  | |  |||| ||||  ||||   ||||||
CACTTGATAGAGCTACTATCAATGCATCTGTTAGAAAAACAAATAGATTGGTGACCATTGAGGAAAGCTTCCCACAGCATGGGATTGGTGCTGAGATATGgtacgctctctctccacatgcattggcacacctgtgtgtggataaggacttttagttctgacactcgttttctttgcag

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G46380.1 (Glycine max), 5'ss of exon 12
CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctctagcccttaccctctcacacatttgtgtgg-tatctattatt--ctaacacatgtttgttgcag---------------------
|||||||| || |  | || ||| | |||||||||||||||||| |  ||||||| |||||||||||||| || || |||||  |||| || || || ||||| | |||   | ||||  |        ||||| ||  | | | ||| |   |||| | ||    |                          
CACTTGATCGATCCACAATCAATACTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtt-tatct---ctttacattgatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacag

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 12
CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttc-tctctagcccttaccct---ctcacacatttgtgtggtatctatta--ttctaaca--catgtttgt-tgcag-------------
| |||||| || |  | || ||||| |||||||||||||||||| |  ||||||| |||||||||||||| || || |||||  |||| || || || |||||  |||||   | ||    |    |   |     || |  ||    |||  |  |  ||  ||| |  || || |              
CGCTTGATCGATCCACAATCAATGCTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttacattgatttgtttttctatgaacgtatcttactggttaactcttggcaatcatatgagtgtgtacttctcttgcacag

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G02380.1 (Glycine max), 5'ss of exon 12
CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttc-tctctagcccttaccct---ctcacacatttgtgtggtatctatta--ttctaacacatgtttgt-tgcag-------------
| |||||| |  |  | || ||| | |||||||||||||||||| |  ||||||| |||||||||||||| || || |||||  |||| || || || |||||  |||||   | |||   |    |   |    ||| |  ||    |||  |  |  ||    |  || || |              
CGCTTGATCGGTCCACAATCAATACTTCTGTCAGGAAAACCAACAGGCTGGTGACAGTTGAAGAAGGGTTTCCTCAGCATGGCGTTGGCGCTGAAATCTGgtttatctctttgcattaatttgtttttgtatgaatgtatcttactggttaactcttggcaatcatgagtgtgtacttctcttgcacag

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 12
CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgtt---ctctctagcccttaccctctcacacatttg----tgtggtatctattattctaacacatgtttgttgcag-------------------------------
| ||||| ||| | || || ||||| || ||||||||||| | | || |||||||||||||||| |||||||| ||||||||  |||| || ||||| |||||    ||| |  | |  |  || |  ||     |    |||| ||    |  ||   |  | |  || |                                    
CCCTTGACAGATCGGCAATCAATGCTTCAGTCAGGAAAACTAGCAGACTGGTGACTGTTGAAGAGGGGTTCCCTCAACATGGTGTTGGCGCTGAGATCTGgttaccttctttttcaccaaatctatggcatgggcgagggtgtgatagtggtggtttagaatcctccttttaagtatttttcttacaacgtgtctgaatttctgcag

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|89754920|gb|DY685537.1|DY685537
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|78092463|gb|DV520837.1|DV520837
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|60394298|gb|DN227168.1|DN227168
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|76915086|gb|DV165815.1|DV165815
EST:     TGGGATTGGTGCCGAGATATG                         CATTTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: TGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|88758101|gb|DY542242.1|DY542242
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|33097928|gb|CF057888.1|CF057888
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|88757272|gb|DY541413.1|DY541413
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|32931889|gb|CF036701.1|CF036701
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|37386471|gb|CF630421.1|CF630421
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|78121283|gb|DV539667.1|DV539667
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|76912074|gb|DV164558.1|DV164558
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|32826620|gb|CD966298.1|CD966298
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|211088145|gb|FL307530.1|FL307530
EST:     GACTGTTTGAAGAAAGGTTCCCCACACCATGGGATCGGTGCCGAGATATG                         CATGTCTGTTGTAG
genomic: GACTGTT-GAAGAAGGGTTCCCC-CAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAG
EST: gi|32829636|gb|CD969314.1|CD969314
EST:     GTGACTGTTGAAGAAGG-TTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAA-CGTTCGCGT
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGC-TTCGCGT
EST: gi|86473456|gb|DY239826.1|DY239826
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCCCCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
EST: gi|32829111|gb|CD968789.1|CD968789
EST:     GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAA-CGTTCGCGT
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGC-TTCGCGT
EST: gi|211019433|gb|FL375798.1|FL375798
EST:     GTGACTGTTGAAGAAGGTTTCCCCCAACATGGGATTGGTGCCGAGATATG                         CATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG
genomic: GTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAG

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: 100

CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102

CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctcta ... tttgttgcagCATGTCTGTTGTAGAAGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCCAACATGGGATTGGTGCCGAGATATGgttctctctagcccttaccctctcacacatttgtgtggtatctattattctaacacatgtttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG