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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGTGAACGAGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtgctcgtaatggattgatgacgaaggactgaggcgtgtcttattcgaaggttgatgcttgcttgccaacctttgctgctgcgcacgttccct...

Basic information

species Zea mays
transcript GRMZM2G425986_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G425986_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g10850.1 (Oryza sativa), 5'ss of exon 2
GAGGTGAACGAGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtgctcgtaatggattgatgacgaaggactgaggcgtgtcttattcgaaggttgat-gcttgcttgccaacctttgctgctgcgcacgttccct-
||||||||||||||||||||||| || || || ||||| ||||||||||||||||| ||||||||| | |    | || |||     |   | |   ||  ||      ||| | | |  | |  |||| |        | || ||  |||| | |   |  
GAGGTGAACGAGATGTGGGCGGGGCTCGGGTATTACCGGAGGGCTCGATTTCTGCTCGAGgtgagtagcgagt-tgattgatcacgaattcatggtcgaaacgacggggattgggatgaggttcacttgttcagtgcgttctg-tggagcgcccatgaaccg
















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|76932963|gb|DV173258.1|DV173258
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|71323508|gb|DR798415.1|DR798415
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|71299540|gb|DR785778.1|DR785778
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|50329302|gb|CO524428.1|CO524428
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|91874808|gb|EB404765.1|EB404765
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|211280029|gb|FL236952.1|FL236952
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTARGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTT
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTT
EST: gi|76285023|gb|DV024591.1|DV024591
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|71441857|gb|DR822907.1|DR822907
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|78090907|gb|DV519281.1|DV519281
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|76926659|gb|DV170957.1|DV170957
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|71323967|gb|DR798666.1|DR798666
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|78103468|gb|DV521896.1|DV521896
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|74245470|gb|DT653384.1|DT653384
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|76920658|gb|DV168270.1|DV168270
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|71446168|gb|DR827218.1|DR827218
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|211281830|gb|FL236960.1|FL236960
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|94478908|gb|EB707866.1|EB707866
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTG
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTG
EST: gi|211280023|gb|FL236946.1|FL236946
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|6865197|gb|AW360547.1|AW360547
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGGTGTTTCCTCGCACAGCATTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
EST: gi|211280026|gb|FL236949.1|FL236949
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCA-ATCATCNGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATC-GAAAAGGGGTTGTTTCCTTGCACGGCGTTAGC
EST: gi|211280024|gb|FL236947.1|FL236947
EST:     AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAG                         GGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC
genomic: AGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCC

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 3 RNA-Seq libraries.


Block sizes: 30 (upstream exon), 46 (downstream exon)
Score: 16

GAGGTGAACGAGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCCCTTCGTGAGGTTCGTGGCATTGGGGATTACACAGCTGGAGCAATCGCTT


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 4

GAGGTGAACGAGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCCCTTCGTGAGGTTCGTGGCATTGGGGATTACACAGCTGGAGCAATCGCTT


Block sizes: 43 (upstream exon), 43 (downstream exon)
Score: 6

GAGGTGAACGAGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtg ... ggagaaacagGGAGCAAAGCAGATCATCGAAAAGGGGTTGTTTCCTTGCACGGCGTTAGCCCTTCGTGAGGTTCGTGGCATTGGGGATTACACAGCTGGAGCAATCGCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGTGAACGAGATGTGGGCGGGTCTTGGCTACTACCGTAGGGCTCGATTTCTGCTGGAGgtgagttgtgctcgtaatggattgatgacgaaggactgaggcgtgtcttattcgaaggttgatgcttgcttgccaacctttgctgctgcgcacgttccct

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA