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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttccttatcgagtctccattccctatccactcattttgcagcgaatgtactgcccgatgtgcgtgcatgactaggcacttactctggggaccaa...

Basic information

species Zea mays
transcript AC217358.3_FGT005
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217358.3_FGT005 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 5'ss of exon 2
TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc-ttatcgagtctccattccctatccac-tcattttgcagcgaatgtactgcccgatgtgcgtgcatgactaggcacttactctggggaccaa
|||| | |||||||||||| |||| ||||||||||||||||| ||||| ||||| |||||||||||||||||||| || |||||||| || |||||||||||||  |||  |  | |    |    |  ||  | |  |||| | |  | ||   |  |    |  |   ||  | |   |     |   | ||     | |
TCACTTCATGATCCCGTGGTTCGAGAGGCCGATCATCTACGATGTCCGAGCCCGCCCCAACCTCGTCGAGAGCACTTCTGGAAGCCGTGATCTCCAGATGgtaaaattctgtccttgcacttggggtttctgactaggtcatgtcgttgagatgatgat--ttgtagcatgtagaaggtgatttgttggttgtgatttgcga

upper sequence: AC217358.3_FGT005 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g60000.1 (Oryza sativa), 5'ss of exon 2
TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc-ttatcgagtctccattccctatccac-tcattttgcagcgaatgtactgcccgatgtgcgtgcatgactaggcacttactctggggaccaa
|||  | ||||||| || | |||| ||||||||||||||||| ||||| ||||| |||||||||||||||||||| || |||||||| || |||||||||||||  |||   | | |    |    |   |  | |  | || | |  | || || |      |  |   ||  | |   |     |   | ||     |||
TCAATTCATGATCCTGTTGTTCGAGAGGCCGATCATCTACGATGTCCGAGCCCGCCCCAACCTCGTCGAGAGCACTTCTGGAAGCCGTGATCTCCAGATGgtaaaattctgctgttgcacttggggtttgtgactaggttatgtcgttgaga-tg-atcatttgtagcatgtagaaggtgatctgttggttgtgatttgcaa

upper sequence: AC217358.3_FGT005 (Zea mays), 5'ss of exon 2
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 5'ss of exon 3
TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttccttatcgagtctccattccctatccactcattttgc------agcgaatgtactgcccgatgtgcgtgcatgactaggcactta----ctctggggaccaa----------
 ||||| ||||| || ||| | ||||||||| ||||||| ||||| || || |||||  |||| || ||||| || ||||||||||| || || |||||||||  | | ||| |       |||||  |  ||   |  |||||       || ||||||   | |    |      ||| | || || ||||     | || ||    |          
ACACCTTATGATTCCTTGGTTTGAAAGGCCGGTCATCTATGACGTTCGTGCTCGACCTTACCTTGTTGAGAGTACATCCGGAAGCCGTGATCTTCAGATGgtac-tctgcttctactcctcccattttcagtcattttgttttgtgaatttagtgaatgtgaagtcgttcgcttcaacatca-taagctcttaagttttttgtggttttaaaactttcag

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|149110344|gb|EE190366.2|EE190366
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|9733307|gb|BE512059.1|BE512059
EST:     GAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: GAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|149076703|gb|EE165347.2|EE165347
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|33092429|gb|CF052423.1|CF052423
EST:     CCGACCCAACCCCGTCGAGAGCACCTCCGGAAGGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCGACCCAACCTCGTCGAGAGCACGTCCGGAA-GCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|15215048|gb|BI431144.1|BI431144
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|78081933|gb|DV510345.1|DV510345
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|148982739|gb|EE028558.2|EE028558
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|71308360|gb|DR790410.1|DR790410
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|18659717|gb|BM500486.1|BM500486
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|149112958|gb|EE295743.2|EE295743
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|6021034|gb|AW065962.1|AW065962
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|6021466|gb|AW066394.1|AW066394
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|78084473|gb|DV512866.1|DV512866
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|19437062|gb|BM953472.1|BM953472
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|31355780|gb|CD440137.1|CD440137
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|20507570|gb|BQ279689.1|BQ279689
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|60398117|gb|DN230933.1|DN230933
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|148987626|gb|EE031500.2|EE031500
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|76011854|gb|DT939024.1|DT939024
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|22715353|gb|BU197718.1|BU197718
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|15214991|gb|BI431123.1|BI431123
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|78079465|gb|DV507877.1|DV507877
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|31664014|gb|CD573194.1|CD573194
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|37418141|gb|CF646734.1|CF646734
EST:     CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|6587642|gb|AW244960.1|AW244960
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|31356533|gb|CD440890.1|CD440890
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|6536621|gb|AW224934.1|AW224934
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGAAGCCGCGACCTCCAGATG                         GTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT
EST: gi|18649915|gb|BM498734.1|BM498734
EST:     CCCGACCCAACCTCGTCGAGAGCACCTCCGGATGCCGCGACCTCCAGATG                         GTGAGAATGGGTCTTCGTGTCCTTACTCGACCCATGCCAGATCAGCTACCT
genomic: CCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 587

TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCTAAAATCTACAGGAACCTGGGGGAGAACTTCAATGAGAGAGTTCTGCCTT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 155

TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCTAAAATCTACAGGAACCTGGGGGAGAACTTCAATGAGAGAGTTCTGCCTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 207

TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCTAAAATCTACAGGAACCTGGGGGAGAACTTCAATGAGAGAGTTCTGCCTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 355

TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttcc ... acttgggcagGTGAGAATTGGTCTTCGTGTCCTTACTCGACCCATGCCAGACCAGCTACCTAAAATCTACAGGAACCTGGGGGAGAACTTCAATGAGAGAGTTCTGCCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACCTGATGATCCCGTGGATCGAAAGGCCGATCATCTACGACGTCCGCGCCCGACCCAACCTCGTCGAGAGCACGTCCGGAAGCCGCGACCTCCAGATGgtaagtttccttatcgagtctccattccctatccactcattttgcagcgaatgtactgcccgatgtgcgtgcatgactaggcacttactctggggaccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG