Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaatccatcggacttcacctcccgtcatctttgtcacttgtcgccgctcagttcgtagttctgtgctgtgatacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG

Basic information

species Zea mays
transcript GRMZM2G054706_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054706_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g04260.1 (Oryza sativa), 3'ss of exon 1
-------gtactaatccatcggacttcacctcc-cgtcatctttgtca------cttgtcgccgctcagttcgtag-------ttctgtgctgtgatacgcctagGCACCGAGGATAA---TAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG
        |||| ||||| ||    || | ||  |||| ||| | ||       ||  |||| |||| |  || |        |||  || | || |     ||||    ||||| ||   |  |||||||||| | || || ||||||||||||||||| |||||| |||||| ||| |  |||
gtgggtactactgatccagcgattctctcttctgcgtcgtctctctctgtgattctactcgctgctctgaccgaatggagattttccttgttttggtcgttgtagGTGGGGAGGAGAAGCGTGACAGCACGATTCTTGAGCTCGCGCAGCTGCTCGACGTGTACGATGATCTCTTCCCTGCTAAG
















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|18649042|gb|BM497861.1|BM497861
EST:     GCGGCCTTCTCACCCTACGCTCCCCCGCCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: GCGGCCTTCTCACCCTACGCT-CCCCG-CCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|211331853|gb|FL370139.1|FL370139
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|74236590|gb|DT644504.1|DT644504
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|88752193|gb|DY536334.1|DY536334
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|71326892|gb|DR800103.1|DR800103
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|76931669|gb|DV172797.1|DV172797
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|89757721|gb|DY687204.1|DY687204
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|88752231|gb|DY536372.1|DY536372
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|50324552|gb|CO519678.1|CO519678
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|211447325|gb|FL371185.1|FL371185
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|93015545|gb|EB641065.1|EB641065
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|60399511|gb|DN232323.1|DN232323
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|211042074|gb|FL383254.1|FL383254
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|71769763|gb|DR967700.1|DR967700
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|18654773|gb|BM499578.1|BM499578
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|93015602|gb|EB641122.1|EB641122
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|211434257|gb|FL404589.1|FL404589
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|71436328|gb|DR817378.1|DR817378
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|76923536|gb|DV169535.1|DV169535
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|211533535|gb|FL409964.1|FL409964
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGA
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGA
EST: gi|71428269|gb|DR809319.1|DR809319
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|37418625|gb|CF646983.1|CF646983
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|211301339|gb|FL414902.1|FL414902
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|149044689|gb|EE047662.2|EE047662
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|76283964|gb|DV023532.1|DV023532
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|93013386|gb|EB638906.1|EB638906
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|21390005|gb|BQ528054.1|BQ528054
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|78081498|gb|DV509910.1|DV509910
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
EST: gi|211217744|gb|FL411417.1|FL411417
EST:     CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCG                         GCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG
genomic: CTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACG

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: 45 (upstream exon), 49 (downstream exon)
Score: 97

GGCTCCGCAGCCGCGGGGAGCCACCTCGACGCGTTCGCCTCCCGCGCCTGCTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

GGCTCCGCAGCCGCGGGGAGCCACCTCGACGCGTTCGCCTCCCGCGCCTGCTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

GGCTCCGCAGCCGCGGGGAGCCACCTCGACGCGTTCGCCTCCCGCGCCTGCTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GGCTCCGCAGCCGCGGGGAGCCACCTCGACGCGTTCGCCTCCCGCGCCTGCTGCGGCCTTCTCACCCTACGCTCCCCGCCGACTTCCCATCCTACGACCGgtactaatcc ... atacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaatccatcggacttcacctcccgtcatctttgtcacttgtcgccgctcagttcgtagttctgtgctgtgatacgcctagGCACCGAGGATAATAGCAGCACGATTTTGGAACTGGCGCAGCTGCTCGACGTTTACGATCATCTCTACCCCGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT