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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtaaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCCAATAAGCAAGATATGGTGAGCCAACCACACTTGACTCCTTCTAACACGA

Basic information

species Zea mays
transcript GRMZM2G113995_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113995_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 3'ss of exon 4
gtctgtaaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCCAATAAGCAAGATATGGTGAGCCAACCACACTTGACTCCTTCTAACACGA
   | |||   |  |   | ||   | || ||     |  | |  || || |   | | |||  |   |    | |||||||||||||  | || ||||||||||||||||||||||||||| ||||| |||||||||| |||||||||                                  
--gtttaataagctattttaagttatgctcatcagatagcttgccttgtt-agtgaagctaaggtttggtggctttgttgcagGCAATCGTTAATGATCCTTTGATGCTTAACAGTGTAATATTGGTATTTGCCAATAAACAAGATATG----------------------------------
















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|211029880|gb|FL404674.1|FL404674
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211290604|gb|FL410977.1|FL410977
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTG
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTG
EST: gi|211461841|gb|FL417627.1|FL417627
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGA
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGA
EST: gi|211198832|gb|FL369949.1|FL369949
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGGC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTG-C
EST: gi|211212184|gb|FL397467.1|FL397467
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|13516073|gb|BG518349.1|BG518349
EST:     AATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: AATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|33103749|gb|CF063709.1|CF063709
EST:     TTGATTCGTTGGATCGAGAGAGAATTGGAAAAGCCAAATCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGT
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGT
EST: gi|211156685|gb|FL406071.1|FL406071
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCC
EST: gi|211363304|gb|FL391107.1|FL391107
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGGANKCTTAACAGTGTAATACTGGTACTTGC
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTG-ATGCTTAACAGTGTAATACTGGTACTTGC
EST: gi|211115280|gb|FL397760.1|FL397760
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAAT
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAAT
EST: gi|211466099|gb|FL374831.1|FL374831
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATTCAAAGATCCT
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAAT-CAAAGATCCT
EST: gi|5055809|gb|AI734696.1|AI734696
EST:     TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAG                         GCAATAATCAAAGATCCTTTGATGCTTAA
genomic: TTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAA

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: 47 (upstream exon), 39 (downstream exon)
Score: 23

ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCCAATAAGCAAGATATGGTGAGCCAACCACACTTGACTCCTTCTAACACGA


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 91

ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCCAATAAGCAAGATATGGTGAGCCAACCACACTTGACTCCTTCTAACACGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 104

ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCCAATAAGCAAGATATGGTGAGCCAACCACACTTGACTCCTTCTAACACGA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 83

ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctgtaaat ... tctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCCAATAAGCAAGATATGGTGAGCCAACCACACTTGACTCCTTCTAACACGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCCAATAAGCAAGATATGGTGAGCCAACCACACTTGACTCCTTCTAACACGA
                                            ttctgtt  CT-rich tract
                              ttaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtaaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcagGCAATAATCAAAGATCCTTTGATGCTTAACAGTGTAATACTGGTACTTGCCAATAAGCAAGATATGGTGAGCCAACCACACTTGACTCCTTCTAACACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA