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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggccgatcggcctgctcaccttgcctgttgtcttgtctactcctgagatccgtgcggccctagtgctgaattctcgtggaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACGTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCTGCTCGCC

Basic information

species Zea mays
transcript GRMZM2G162145_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162145_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g50770.2 (Oryza sativa), 3'ss of exon 1
gtaagtggccgatcggcctgctcaccttgcctgttgtcttgtctactcctgagatccgtgcggccc-----tagtgctgaattctcg--tg----gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACGTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCTGCTCGCC
||||| |  ||  |  || |  | |  |  || |   || |||  ||| |  ||||  || ||| |     | | | ||    ||    ||    |||     ||||||||||||| |  |||||||| |||||||||||||| ||||| ||||| ||||||||||||||||||||||| || ||||| || |||||  | ||||
gtaagcgctcgcgcatcccggcctctct--ctatctcctcgtc--ctcgtaggatctatgtggctcgccggtggcgttgcgcgctaagctgatgtgaaccaacagGGCGACTCGGAGGCGCACTCGCCGGTGGTCTACGACGATGCCGGGGTCACCTACATGTTCATCCAGCACAACAACGTGTTCCTACTAACCGCCTCCCGCC
















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|149015119|gb|EE044881.2|EE044881
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|76911459|gb|DV164280.1|DV164280
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211217159|gb|FL385243.1|FL385243
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211256983|gb|FL408751.1|FL408751
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211263870|gb|FL390550.1|FL390550
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211024700|gb|FL384563.1|FL384563
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211406290|gb|FL425473.1|FL425473
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|148946287|gb|EC891588.2|EC891588
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211360643|gb|FL391093.1|FL391093
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211478803|gb|FL379712.1|FL379712
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211397436|gb|FL369352.1|FL369352
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211526835|gb|FL377023.1|FL377023
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAA                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGANGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|78078571|gb|DV506983.1|DV506983
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|71318385|gb|DR795957.1|DR795957
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|76014626|gb|DT941796.1|DT941796
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211305391|gb|FL411425.1|FL411425
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211348465|gb|FL392077.1|FL392077
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211294477|gb|FL387414.1|FL387414
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211056996|gb|FL387679.1|FL387679
EST:     TCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211315648|gb|FL416761.1|FL416761
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211157041|gb|FL430150.1|FL430150
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|149069970|gb|EE158370.2|EE158370
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|149065604|gb|EE286727.2|EE286727
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|93284149|gb|EB676413.1|EB676413
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|78121823|gb|DV540207.1|DV540207
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211336600|gb|FL396672.1|FL396672
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|211436938|gb|FL408471.1|FL408471
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|148971487|gb|EE022183.2|EE022183
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
EST: gi|71327502|gb|DR800360.1|DR800360
EST:     TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAG                         GGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG
genomic: TCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACG

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: 48 (upstream exon), 49 (downstream exon)
Score: 206

GCTGGACATTAAGGGCCGCGTCCTCGTCTGGCGCGACTATCGTGGTGATGTCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACGTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCTGCTCGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

GCTGGACATTAAGGGCCGCGTCCTCGTCTGGCGCGACTATCGTGGTGATGTCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACGTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCTGCTCGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

GCTGGACATTAAGGGCCGCGTCCTCGTCTGGCGCGACTATCGTGGTGATGTCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACGTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCTGCTCGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

GCTGGACATTAAGGGCCGCGTCCTCGTCTGGCGCGACTATCGTGGTGATGTCTCCGCGCTCCAGGCCGAGCGCTTCTTCACCAAGCTCCTCGACAAGGAGgtaagtggcc ... gaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACGTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCTGCTCGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggccgatcggcctgctcaccttgcctgttgtcttgtctactcctgagatccgtgcggccctagtgctgaattctcgtggaatgggtagGGCGACTCGGAAGTCCACTCGCCTGTGGTCTACGACGACGCCGGCGTCACGTACATGTTCATCCAGCACAACAATGTCTTCCTCCTCACCGCTGCTCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT