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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcagaaacacctcctacttttttccccttcttgttaaacactgacatctcttgactattgtacacgcag

Basic information

species Zea mays
transcript GRMZM5G886989_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os09g06970.1 (Oryza sativa), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcagaaacacctcctacttt-tttccccttcttgttaaacactgacatctcttgactattgtacacgcag
|||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||| ||||| ||||| ||| |   | |  || ||| || |||  |  |  ||  | | |||||  |  |||||||    || | ||||
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGgtaatgaatttaaaattcgtaccttattttgcgcttgtgacaga-actgatgttacttgacttccctatatgcag

upper sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g19060.2 (Oryza sativa), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcagaaacacctcctacttttttccccttcttgttaaacactgacatctcttgactattgtacacgcag-------------------------------------------------------
|||||||||||||||||||||||||||||| |||||||||||||| |||||||||||| | ||||||||||| |||||||||||||| || ||||| ||||| ||| |   | |  || ||| || ||   |   |    ||| |||||  |  |||||||   ||| | ||||                                                       
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAATCTGAAGACTAATCATAGGgtaatgaatgtaaaattcataccttattttgcacttgtgaaaaaactgatgttacttgacttccgtatatgcagggcacatttgttcttcaagataaccatttccggtggcttactcgtgtttctgtag

upper sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g19060.1 (Oryza sativa), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcagaaacacctcctacttttttccccttcttgttaaacactgacatctcttgactattgtacacgcag
|||||||||||||||||||||||||||||| |||||||||||||| |||||||||||| | ||||||||||| |||||||||||||| || ||||| ||||| ||| |   | |  || ||| || ||   |   |    ||| |||||  |  |||||||   ||| | ||||
TCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGACTTTTGGTCAGAGTTATTCAAGAAGCAAATTGACAATCTGAAGACTAATCATAGGgtaatgaatgtaaaattcataccttattttgcacttgtgaaaaaactgatgttacttgacttccgtatatgcag

upper sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G42850.1 (Glycine max), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtga-tgcagaaac---acctcctacttttttccccttcttgt-taaacactgacatctcttgactattgtacacgcag-----------
||| || |  |||||||| || || |||||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||  |||| ||||| || ||||||| | ||||      | | | ||    |      |   | | || | |   | |  | |||| ||  ||  |    |           
TCGGTTCACGGATCATCTCGAGGCCATCAAGTTCATCTGCAAGGATTTTTGGTCTGAGCTCTTCAAGAAGCAGATTGACAACTTGAAGACAAACCATAGGgtgagttcagagctctgatcccttatgggtggtatatatatatatatatatatatagtttttgattaaggtgtatttggttctgttgtag

upper sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
lower sequence: AT3G05000.1 (Arabidopsis thaliana), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgca---gaaacacctcct------acttttttccccttcttgttaaacactgacatctcttgactattgtacacgcag
  | || ||||| ||||| || ||||||||||||||||||||||| || ||||| ||| | ||||||||||||||||| ||| | || ||||||||| |||| |   |   |  |     |||      |        | ||||||||          ||    | || | ||   |   |||
AAGGTTCAGTGACCATCTAGAGGCAATCAAGTTTATCTGCAAAGACTTCTGGTCTGAGGTCTTCAAGAAGCAGATTGATAATTTAAAGACAAATCACCGGgtaagataactgggattttacctgaacaaagaccaaaactcttcttgtgtgtgttattcacagatggaatgtttctc-ttcag

upper sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0030g00700.t01 (Vitis vinifera), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtga-tgcagaaacacctcct-acttttttccccttcttgttaaacactgacatctcttgactattgtacacgcag
 || |||||||||||||| || |||||||||||||||||||| || || ||||| ||||| ||||||||||| || |||||  | || ||||| ||||| |||| | ||  ||       | | ||    |    | |||||       ||  |  ||| |   |||| |  | ||
CCGGTTTAGTGATCATCTAGAGGCAATCAAGTTTATCTGCAAGGACTTCTGGTCTGAGCTCTTCAAGAAGCAAATAGACAACTTAAAGACAAACCACAGAgtgagttcaagaatttgaaatgaattgaaacttggttttgttgtctgaagaagtggctt-atgcttgt-cttgtag

upper sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
lower sequence: EFJ20859 (Selaginella moellendorffii), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcagaaacacctcctacttttttcccct-tcttgttaaacactgacatctcttgactattgtacacgcag--------
 ||||| |  |||||  | ||||  |||||||| || ||||| ||||| ||| | ||| | ||||||||||||||||||||||| |||||||||||| |||| | ||| |||||     || |||||  | || |||  |  |   |||   |   ||  || || |    |           
GCGATTCACAGATCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAATCTCAAAACAAATCACCGGgt-acgcaaaaacaaactttagtttttctcgctctctcatccattgctggttttgttttcctcttttgtgtgataactcccag

upper sequence: GRMZM5G886989_T03 (Zea mays), 5'ss of exon 3
lower sequence: EFJ32385 (Selaginella moellendorffii), 5'ss of exon 2
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcagaaacacctcctacttttttcccct-tcttgttaaacactgacatctcttgactattgtacacg-cag-------
 ||||| |  || ||  | ||||  |||||||| || ||||| ||||| ||| | ||| | ||||||||||||||||||||||| |||||||||||  |||| | ||| |||||     || |||||  | || |||  |  | | |||   |   ||  || || |    | ||        
GCGATTCACAGACCACTTGGAAGTCATCAAGTTCATATGCAAGGATTTCTGGGCGGAGGTTTTCAAGAAGCAGATTGACAATCTCAAAACAAATCATCGGgt-acgcaaaaacaaactttagtttttctcgctctctcatccatcgctggttttgttttcctcttttgtgtgacaactcccag

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|78086281|gb|DV514674.1|DV514674
EST:     TGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: TGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|60343078|gb|DN210051.1|DN210051
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|60350952|gb|DN217925.1|DN217925
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|88752115|gb|DY536256.1|DY536256
EST:     AAACAAATCACAGG                         GGTGCCTTTGTCTTTCAAGATAACCGTTTTCGGTGGGTTACTCGTGTTTCT
genomic: AAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|60342045|gb|DN209018.1|DN209018
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|60355961|gb|DN222934.1|DN222934
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|78075052|gb|DV503486.1|DV503486
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|89248854|gb|DY620640.1|DY620640
EST:     TTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: TTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|50334363|gb|CO529489.1|CO529489
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|211101165|gb|FL105401.1|FL105401
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCAGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|60343072|gb|DN210045.1|DN210045
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
EST: gi|60355163|gb|DN222136.1|DN222136
EST:     GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGG                         GGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT
genomic: GGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCT

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: 104

TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCTCTAGATCCACGTACAGAGAACACAGATTCAACTGAAAATGATTCTGCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 78

TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCTCTAGATCCACGTACAGAGAACACAGATTCAACTGAAAATGATTCTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCTCTAGATCCACGTACAGAGAACACAGATTCAACTGAAAATGATTCTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcaga ... gtacacgcagGGTACCTTTGTCCTTCAAGATAACCGTTTTCGGTGGCTTACTCGTGTTTCTCTAGATCCACGTACAGAGAACACAGATTCAACTGAAAATGATTCTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGATTTAGTGATCATCTTGAAGCAATCAAGTTTATCTGCAAAGATTTTTGGTCAGAGCTGTTCAAGAAGCAGATTGACAATCTGAAAACAAATCACAGGgtgatgcagaaacacctcctacttttttccccttcttgttaaacactgacatctcttgactattgtacacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT