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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtcaaagaagctttctcgcatcaatttgagtatcagagtatgacactgattcagactgttgcttctgaaaccatgttttacag

Basic information

species Zea mays
transcript GRMZM2G063676_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 5'ss of exon 8
GGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgt-tgtcaaagaagctttctcgcatcaatttgagtatcagagt-atgacactgattcagactgttgcttctgaaaccatgttttacag
|| | | |||||   ||||||||||||| || ||||| |||||  | |||||||| ||  |  |||| ||  ||||||||||||||||||||||||||||||| || |||  |       |  |  ||   |  ||| | | ||  | ||     ||  | || |   | | ||| ||||| ||||| ||||
GGCTAATAGAGAAACAGCAGCAGCAGGATGCTCTACCAAAGCATGCTGATCCTGTCCTCTTAATATCTGACATGAAGAAGAAAGCTGAAGCACTTGACAGgtttgtgtgtttatttgctataataacac--acctga-tgttagtttgattcttgtgtctgagtcaactacctct-aaaccttgtttcacag
















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|17931137|gb|BM268097.1|BM268097
EST:     AAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: AAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|71301428|gb|DR786744.1|DR786744
EST:     AGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: AGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|67032698|gb|CO461447.1|CO461447
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|31355540|gb|CD439897.1|CD439897
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|24769887|gb|CA405016.1|CA405016
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|211150159|gb|FL276364.1|FL276364
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|67011904|gb|CO440653.1|CO440653
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|7145128|gb|AW506609.1|AW506609
EST:     GAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: GAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|71759979|gb|DR957916.1|DR957916
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|71307555|gb|DR789996.1|DR789996
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|88750857|gb|DY534998.1|DY534998
EST:     CTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|211148733|gb|FL276359.1|FL276359
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|60396368|gb|DN229237.1|DN229237
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|89758537|gb|DY687684.1|DY687684
EST:     CTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|4612879|gb|AI603718.1|AI603718
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCCCTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|211148735|gb|FL276361.1|FL276361
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|78023494|gb|DV491881.1|DV491881
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAT
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|5608414|gb|AI901991.1|AI901991
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|211148736|gb|FL276362.1|FL276362
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|47962664|gb|CN845373.1|CN845373
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
EST: gi|211352366|gb|FL462348.1|FL462348
EST:     CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAG                         GTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC
genomic: CCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGAC

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), 48 (downstream exon)
Score: 125

GGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGACTCCGCCACCACATACTCCACCTCCACAGCCTGAAGCCCAAGCATCTGAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 51

GGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGACTCCGCCACCACATACTCCACCTCCACAGCCTGAAGCCCAAGCATCTGAC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 21

GGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGACTCCGCCACCACATACTCCACCTCCACAGCCTGAAGCCCAAGCATCTGAC


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 61

GGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtc ... tgttttacagGTTCTGCAAACCGATCATGACTAAACCAAAGCCAGCTCCGAAGCCACAGACTCCGCCACCACATACTCCACCTCCACAGCCTGAAGCCCAAGCATCTGAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGAGAGAGAGGAAGCAGCAGCAGGACGCCCTACCTAAGCACACCGATCCTGTGCTGCTCGTATCAGATCTGAAGAAGAAAGCTGAAGCACTTGACAGgttcgttgtcaaagaagctttctcgcatcaatttgagtatcagagtatgacactgattcagactgttgcttctgaaaccatgttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC