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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgccaattacgttcttgctattgaattatggccgattgtttgtgaaactggacatttaatttaatttttcag

Basic information

species Zea mays
transcript GRMZM5G868433_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 5'ss of exon 4
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgccaatta-cgttcttgctat----tgaattatggc---cgattgtttgtgaaactggacatt--taatttaatttttcag
||||||||||||||| || |||||||||||||| |||||||||||||| ||||||||||| |||||   ||  |   |||||   |     |||| | | ||   || | || | | ||  | |   ||  |  ||| ||| | |||
TATCAATGCCATGCACCCCAAGACCAGGAAGATCTTGCAGCTTCTGCGGTTGAGGCAGgttggtttatgaaccagttttcttagaaatgcgtgaactcttgcgtacgctggtgtattaactttgtgcttaattgtttgattctacag

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 5'ss of exon 3
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttg------ccaattacgttcttgc---tattgaa-ttatggccgattgtttgtgaaactggacatttaatttaatttttcag
||||||||||||||| || |||||||||||||| ||||||||  |||||||||||||||||||| ||       |||| |  |   |||   | ||||| |||||    | |  | || ||    |  |   |  |||||||| |||
TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAGgtgggtgtggttttcacaatcatttgaatgcacgtgttgaaattatgatatagtact-gtcaattgaggaaaaaatgttaattttgcag

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G18170.1 (Glycine max), 5'ss of exon 4
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgg--gtttgccaattacgttcttgctattgaattatggccgattgtttgtgaaactg--gacatttaatttaatttt--tcag------------------
||||||||||||| |||| || || ||||||||  ||||||||||||||||||| |||||    | || | ||||||    |     ||   || | |  | |   || |  || ||  |  | |    || || ||  |||                   
TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaactgcttacaaattacaaaatgagattt---tttttgttggtcacttattgaattgctgttactggtattgatcttaatcaatgctagtaagtaacttga

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G06860.1 (Glycine max), 5'ss of exon 4
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtt--tgccaattacgttcttgctattgaattatggccgattgtttgtgaaactg--gacatttaatttaatttt--tcag-----------------
||||||||||||| ||||||| || ||||||||  ||||||||||||||||||| |||||    |  |  ||| |||  | |||  |||   || | |  | |   |||   || ||  |  | |   ||| || ||  |||                  
TATCAATGCCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactacttacaaatacaat-ttgagattct-tttttgttggtcacttgatgaattgctgctagtgtttttgatcttaatcaatgcttgtaagtaacttg

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 5'ss of exon 4
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgg-gtttgccaattacgttcttgctat-----tgaattatggccgattgtttgtga-------aactggacatttaatttaatttttcag--------
 |||||||| ||||| || |||||||||||||| ||||||||||| || ||||| |||||   | |||  | ||   ||  || | |     ||  || |   |  || | | | |       |||||||||   ||     || | | |        
GATCAATGCTATGCACCCGAAGACCAGGAAGATTTTGCAGCTTCTACGATTGAGACAGgtaaagattgatacttttttttgtgttttctttttggtttttttgctcttttctttaataattataactggacaaaaaaaaagtttctgctgatggtttt

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 4
lower sequence: EFJ23123 (Selaginella moellendorffii), 5'ss of exon 3
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgccaattacgttcttgctattgaattatggccgattgtttgtgaaactggacatttaatttaatttttcag
|||||| | ||||||||| |||||| ||||||| ||||||||||| ||  || | |||||   ||        | ||   ||| ||||   ||    ||| |  |  |   |    |   ||  ||| ||       
TATCAACGACATGCATCCCAAGACCCGGAAGATCTTGCAGCTTCTTCGCCTGCGTCAGgtaaattccttgtgaaagt---tgcgattgtgata----cgagttctcttactatcacattctttcttttatag-----

upper sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 4
lower sequence: EFJ20182 (Selaginella moellendorffii), 5'ss of exon 3
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgccaattacgttcttgctattgaattatggccgattgtttgtgaaactggacatttaatttaatttttcag
|||||| | ||||||||| |||||| ||||||| ||||||||||| ||  || | |||||   ||        | | |     | |  ||  |  |     ||  | | |   |     ||| ||            
TATCAACGACATGCATCCCAAGACCCGGAAGATCTTGCAGCTTCTTCGCCTGCGTCAGgtaaattccttgtgaaagctgcgattgtgaaacga--gttctctgactatcacgttctttcttttatag----------

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|15632349|gb|BI679442.1|BI679442
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211173109|gb|FK956294.1|FK956294
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTKAGGCAG                         ATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|94477419|gb|EB706377.1|EB706377
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211173107|gb|FK956292.1|FK956292
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211171435|gb|FK956283.1|FK956283
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|166438461|gb|EG182561.1|EG182561
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATATTCAATGGCGTGTTCC
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCC
EST: gi|15590144|gb|BI674760.1|BI674760
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211173119|gb|FK956304.1|FK956304
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATATTCAATGGCGTGTTCCTGAAAGTCAACANG-CTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211171440|gb|FK956288.1|FK956288
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGARGCAG                         ATCTTCAATGGCGTGTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTT
EST: gi|211173115|gb|FK956300.1|FK956300
EST:     CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATATTCAATGGCGTGT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGT
EST: gi|20299953|gb|BQ162896.1|BQ162896
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGAGTGTTCCTGAAAGTCAACAAAGCAACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|211173112|gb|FK956297.1|FK956297
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGC
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGC
EST: gi|9733002|gb|BE511754.1|BE511754
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
EST: gi|15313739|gb|BI478933.1|BI478933
EST:     CCATGCACCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG                         ATCTTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT
genomic: CCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTT

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: 1571

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1492

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1257

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 841

TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgc ... aatttttcagATATTCAATGGCGTGTTCCTGAAAGTCAACAAGGCTACCATTAACATGCTTCGCAGGGTTGAGCCTTATGTTGCATATGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAGgtgggtttgccaattacgttcttgctattgaattatggccgattgtttgtgaaactggacatttaatttaatttttcag

- - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - GCAGCT