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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgttgctagtacggttgatcagctgagctgcttcttgatctttgcctagtacgaagcaaagccccttagtgcctgaaccctttttcttcttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA

Basic information

species Zea mays
transcript GRMZM2G007489_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g05130.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------------------------------acgttgctagta---cggtt---gatca---gctgagctgcttcttgatctttgcctagtacgaagcaaagccccttag-tgcctga--accctttttcttcttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA
                                                                  |||   |||||     |||     |||   ||  |||||  |    |   ||||   |||      |||||   | |  |  ||||  ||  ||| | || || | | ||||||||||| ||  |||| ||||||||||||||||| |||||||||||  ||||||||||||||||||| || || ||||| ||||| |||||||| ||| 
gtaacttctttttccttttctctatccgaacatgctatctctagatcagaaaagagagtgtctgatcgtaattagtaacctagttcctagtcatatgccaagctg--taaaaacacttgcactgtatattcaaaagctattcaaatttctgagtacgttttgtttttttttcctcagAGTGCTCCAATTTCGATACTGGAGAAGCACGAGCTTGCAAGCATGACCTTGGATTACAGGAAGGAGTGTGGCCGTGACAGTGTGCTTCAGTCGCTTACCG

upper sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g43090.4 (Oryza sativa), 3'ss of exon 7
--acgttgctagtacggttgatcagctgagctgcttcttgatctttgcctagtacgaagcaaagccccttagtgcctgaaccctttttc-ttcttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA
           |||  ||||||    ||   |   |||| |  | ||   |||  ||||     |      ||  ||||   |||| |  || ||   | ||||||||||| ||  |  | ||||||||||| ||||| ||||||||||| |||||||||||||||||||| || || |||||||||||||| || || ||||
tctgaccatctgtattgttgat--attgtcattagtctt-acatctggtcagtcagaaggctttcaaacatgtttctgagttctttctaattttttcccccagAGTGCTCCAATTTCAGTACTGGAGAAGCATGAGCTTGCAAGCATGACCCTGGATTACAGGAAGGAGTGTGGCCGAGACAGCGTGCTGCAATCACTTACCA

upper sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g43820.1 (Oryza sativa), 3'ss of exon 6
--acgttgctagtacggttgatcagctgagctgcttcttgatctttgcctagtacgaagcaaagccccttagtgcctgaaccctttttc-ttcttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA
           |||  ||||||    ||   |   |||| |  | ||   |||  ||||     |      ||   |||   |||| |  || ||   | ||||||||||| ||  |  | ||||||||||| ||||| ||||||||||| |||||||||||||||||||| || || |||||||||||||| || || ||||
tctgaccatctgtattgttgat--attgtcattagtctt-acatctggtcagtcagaaggctttcaaacatgtttttgagttctttctaattttttcccccagAGTGCTCCAATTTCAGTACTGGAGAAGCATGAGCTTGCAAGCATGACCCTGGATTACAGGAAGGAGTGTGGTCGAGACAGCGTGCTGCAATCACTTACCA

upper sequence: GRMZM2G007489_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 6
acgttgctagtacggttgatcagctgagctgcttcttgatctttgcctagtacgaagcaaagccccttagtgcctgaaccctttttcttcttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA
  | |  |  |     |    ||   |   |     ||   ||    || |   ||   |  | |  |        ||    |  |  |  |  | ||||||||||||  |  | ||| ||||||  ||||||||  |   |||||| ||||| ||||||| |||||| ||| | ||||| ||||||||||| |||||  
gtgattttcttgtatcttccaagtctaagagtactctgcatttcttttatttataatttacacacaatttgattgaaaggtctcatgatggttgttgcagAGTGCTCCACTGCCAATCTTGGAGAGTCACGAGCTTTCTTCCATGACTCTGGAGTACAGGAGGGAGTGTGGAAGGGACAGTGTGCTGCAGTCCCTCACTG

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|71449548|gb|DR830598.1|DR830598
EST:     ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG                         AGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
genomic: ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
EST: gi|21480804|gb|BQ577487.1|BQ577487
EST:     ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG                         AGGGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
genomic: ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
EST: gi|166534973|gb|EG175451.1|EG175451
EST:     ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG                         AGTGCTCCGATCGCGATCCTGGAGAAG
genomic: ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAG
EST: gi|87154342|gb|DY399131.1|DY399131
EST:     ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG                         AGTGCTCCGATCGCGATCCTGG
genomic: ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGG
EST: gi|26455441|gb|CA827024.1|CA827024
EST:     ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG                         AGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
genomic: ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
EST: gi|6021504|gb|AW066432.1|AW066432
EST:     ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG                         AGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACACTG
genomic: ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
EST: gi|21390363|gb|BQ528412.1|BQ528412
EST:     ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG                         AGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
genomic: ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
EST: gi|76282744|gb|DV022312.1|DV022312
EST:     ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAG                         AGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG
genomic: ATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTG

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: 157

CCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA


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

CCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 31

CCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA


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

CCTAGGTGGTGGGGTGACCTTGATGTCAACCAGCACGTGAATAACGTCAAGTACATCGGTTGGATTCTTGAGgtaatttctt ... ttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctagtacgaagcaaagccccttagtgcctgaaccctttttcttcttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA
                           cctgaaccctttttct  CT-rich tract
                                    tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgttgctagtacggttgatcagctgagctgcttcttgatctttgcctagtacgaagcaaagccccttagtgcctgaaccctttttcttcttcttcgcagAGTGCTCCGATCGCGATCCTGGAGAAGCACGAGCTCGCAAGCATGACGCTGGATTACAGGAAGGAGTGCGGACGCGACAGCGTGCTGCAGTCGCTCACCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-cgttgct
- - - - - - - - - -tcagctg
- - - - - - - - - - - - - -gctgctt
- - - - - - - - - - - - - - - - - - - - - -tgcctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - aagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctgaa