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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatgttaacatgagtcggcggcctttctatgtttggacaagtctgagagccttgcaactcggtagtttctgatcaaaagatatttaattatattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG

Basic information

species Zea mays
transcript GRMZM2G109624_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 11
-ccatgttaacatgagtcggcggcctttctatgtttggacaagtctgagagccttgcaactcggtagt--ttctgatcaaaagatatttaattatattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG
   |||||   ||             | |||  || ||| |      |         | || | |     ||||||| ||| | |||||   | |  || ||||||||||||||||| ||||||||||||||||| |||||||| ||||||  ||||||| ||| ||||||| |  | ||| |  ||||||||||| |||| |
attatgtttgtatctactaattag--tcctagattgggaaacaaagaaacaaaaaaaatcttgattactgttctgattaaacg-tatttggctgttcttccagGTTGATGCTTGTGCTCATCCATTCTTTGATGAACTGCGGGATCCCAAGACCTGCTTGTCAAATGGACGATCATTACCACCCTTGTTCGACTTCTCAGCTG
















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|213179091|gb|FM180755.1|FM180755
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|60399462|gb|DN232274.1|DN232274
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|31664051|gb|CD573231.1|CD573231
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCGCTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|32944815|gb|CF049634.1|CF049634
EST:     GTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: GTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|5607686|gb|AI901353.1|AI901353
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|116824778|gb|EC868424.1|EC868424
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|12973361|gb|BG268442.1|BG268442
EST:     TCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: TCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|60354737|gb|DN221710.1|DN221710
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|60338924|gb|DN205897.1|DN205897
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|21626337|gb|BQ621258.1|BQ621258
EST:     ATCTCGTGTCAAGCCTACTTCAGTACTCACCAAACCTGCGCTGCCCTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|78025807|gb|DV494194.1|DV494194
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC

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: 882

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 202

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagagccttgcaactcggtagtttctgatcaaaagatatttaattatattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG
                                              tattttc  CT-rich tract
                  tagtttctgatcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatgttaacatgagtcggcggcctttctatgtttggacaagtctgagagccttgcaactcggtagtttctgatcaaaagatatttaattatattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
-catgtta
- - - - - - - - cggcggc
- - - - - - - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - ccttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcaaaa