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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagcccacgaataatccgaagcatgctgggtgattcagcgcttcggcaatcagcaccatcatctaacgtctctctcattatgcag

Basic information

species Zea mays
transcript GRMZM2G004528_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 8
CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagcccacgaataatccgaagcatgctgggtgattcagcgcttcggcaatcagcaccatcatctaacgtctctctcattatgcag-------------------------
||||||||| |||||||| ||||| ||||| |||||||| || |||||||||||||| || ||||||||||||||||| ||| | ||| | |||||   ||||||||  |    ||   | ||       ||  |   || ||   || |||||   |||| |  |     |      | | ||||  |                         
CAACACCTGTGAGGACTCACTCCTTGCCGCGCCGATCATTCTTGATCTGGTGCTCCTTGCCGAGCTCAGCACCAGGATTCAGCTGAAAGCCGAGGGGGAGgtaagagttct--gatggactgagatcaattgact--ctctgctgctctgcaattgccaccctttttgccagcaaaattgactatgttgttgtttcacttgttatcctgtgcag

upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 8
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 5'ss of exon 8
CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagcccacgaataatccgaagcatgctgggtgattcagcgcttcggcaatcagcaccatcatctaacgtctctctcattatgcag
||| |||||||||||||| ||| | || || || |||||| | ||||| || ||||| || ||||||||||||||||||||||| ||| | ||||||  |||  |   |     | | | |     ||  |||||   || |   |     || |       | || |   |   |     ||  ||||
CAATACCTGCGAGGACTCTCTCTTAGCTGCTCCAATCATCTTGGATCTTGTTCTCCTCGCGGAGCTCAGCACCAGGATCCAGTTCAAATCCGAGGGAGAGgttcg--tcagttcacagtacatgttattttgggtt-ctctgttttcactgaaccgcggttttgatgttttgaaacatctttttggcag

upper sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 8
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 5'ss of exon 8
CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagcccacgaataatccgaagcatgctgggtgattcagcgcttcggcaatcagcaccatcatctaacgtctctctcattatgcag
|||||||||||||||||| ||| | || || || |||||| | ||| |||| || || ||||||||||||||| | |||||| | ||| |||| |||  |||  |    |      |  |  | |    |    || ||  |   ||   ||         || ||  |  |  | |   ||| |||||
CAACACCTGCGAGGACTCACTCTTAGCTGCTCCCATCATCTTGGATTTGGTCCTTCTTGCTGAGCTCAGCACCCGCATCCAGCTCAAAGCTGAAGGAGAGgtctgttttcttctgcatccttatgggaccctcttgctttggt-ttttaccatcacatggaatgattcataggatgttcaattttgcag

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|13388668|gb|BG462341.1|BG462341
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|32856301|gb|CD995982.1|CD995982
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGCTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTAC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTAC
EST: gi|6022235|gb|AW067163.1|AW067163
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|6021982|gb|AW066910.1|AW066910
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCNCCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|110941538|gb|EE161695.1|EE161695
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|110217273|gb|EC899171.1|EC899171
EST:     TGCTCCTGGCTGAGGTCAGCCCCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCTTTCCACCCGGTGGCCACCATCCTTAGGTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|13388670|gb|BG462342.1|BG462342
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|6022029|gb|AW066957.1|AW066957
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|16919889|gb|BM074405.1|BM074405
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|6022307|gb|AW067235.1|AW067235
EST:     TGCTCCTGGCTGAGCTCAGCNCCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|6637095|gb|AW261367.1|AW261367
EST:     TGCTCCTGGCTGAGCTCAGCACCACGATCCAGCTAAAACCGGAGGGAACG                         GACAAGTTCCACTCCT
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCT
EST: gi|6021766|gb|AW066694.1|AW066694
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|71756431|gb|DR954368.1|DR954368
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|91871596|gb|EB401553.1|EB401553
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|71771141|gb|DR969078.1|DR969078
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|6022274|gb|AW067202.1|AW067202
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|6022096|gb|AW067024.1|AW067024
EST:     TGCTCCTGGCTGAGCTCAGCCCCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|32854168|gb|CD993849.1|CD993849
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGCTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|149071426|gb|EE159821.2|EE159821
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|13515776|gb|BG518052.1|BG518052
EST:     GAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: GAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|13515973|gb|BG518249.1|BG518249
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|60397539|gb|DN230355.1|DN230355
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|148952105|gb|EC897897.2|EC897897
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|21621348|gb|BQ619354.1|BQ619354
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|6021614|gb|AW066542.1|AW066542
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|32854394|gb|CD994075.1|CD994075
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGCTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|148928580|gb|EC873008.2|EC873008
EST:     TGCTCCTGGCTGAGCTCAGCCCCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
EST: gi|148936902|gb|EC881051.2|EC881051
EST:     TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACG                         GACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC
genomic: TGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACC

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), 49 (downstream exon)
Score: 222

CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 123

CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagccc ... cattatgcagGACAAGTTCCACTCCTTCCACCCGGTGGCCACCATCCTTAGCTACCTCACCAAGGCACCACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACACCTGCGAGGACTCGCTCCTCGCCGCACCGATCATCCTCGATCTGGTGCTCCTGGCTGAGCTCAGCACCAGGATCCAGTTAAAACCTGAGGGAACGgtaagagcccacgaataatccgaagcatgctgggtgattcagcgcttcggcaatcagcaccatcatctaacgtctctctcattatgcag

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