Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtaaattcttaaaacatcttttgggtttcccactgtttcaatagttctcagttaactctgtaatttatggttatacactggtcatacttgagtaagtcttgctagtaggaagatgcccttacacttgtcctttgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTCCTCCTTTATTGGCCGTGCTTCAACTAAGAACAAGGGCAGAATGGCTCGT

Basic information

species Zea mays
transcript GRMZM2G144995_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 5
gttggtaaattcttaaaacatcttttgggtttcccactgtttcaatagttctcagttaactctgtaatttatggttatacactggtcatacttgagtaagtcttgctagtaggaagatgcccttacacttgtcctttgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTCCTCCTTTATTGGCCGTGCTTCAACTAAGAACAAGGGCAGAATGGCTCGT
         || |||||||    |   | ||||    |   ||   | |||  ||| |||| | |      | |||  | | |  | ||  | |||||    |                  ||||  ||| |    | ||  |||| ||| |||||||| | ||||| || ||||||||||| |||||||||||||| ||||| ||||||||||||||||| |||||||| |||||||||||| | 
--------gttgttaaaactgact---gatttcttggtagctctcaaattccaagt-aactgtatggaaagttgtttcaaagtactgatcatagagtatacgtcaac------------ttcttatgcttctttactttctcccagGGCATTGAAAACTAGGGGGAATACGCCAAAGTATGGCCTTATATTCCACTCATCCTTCATTGGCCGTGCTTCAACCAAGAACAAAGGCAGAATGGCTAGA
















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|60398604|gb|DN231420.1|DN231420
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCGTATTCAG                         AGCACTGAAAACT
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACT
EST: gi|67014948|gb|CO443697.1|CO443697
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|31406045|gb|CD484777.1|CD484777
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|19822271|gb|BQ048295.1|BQ048295
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|6501106|gb|AW202479.1|AW202479
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|4776651|gb|AI665654.1|AI665654
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|21843447|gb|BQ704028.1|BQ704028
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCA
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCA
EST: gi|29577152|gb|CB617264.1|CB617264
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|31440888|gb|CD510319.1|CD510319
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|29576730|gb|CB616842.1|CB616842
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGNGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|22546099|gb|BU098420.1|BU098420
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|22819971|gb|BU500061.1|BU500061
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|22542401|gb|BU092839.1|BU092839
EST:     TGTGCAGCCTCCCCCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCCCTGAAAACTCGAGGGAACCCCCCAAAGTATGGGCTTATATTCCCCTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|22542271|gb|BU092709.1|BU092709
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|29543471|gb|CB605557.1|CB605557
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|14717533|gb|BI245183.1|BI245183
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|22521189|gb|BU080000.1|BU080000
EST:     TGTGCAGCCTCCCCCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCCCTGAAAACTCGAGGGAACCCCCCAAAGTATGGGCTTATATTCCCCTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|30306737|gb|CD001410.1|CD001410
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|32936238|gb|CF041050.1|CF041050
EST:     TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC
EST: gi|22546098|gb|BU098419.1|BU098419
EST:     TGTGCAGCCTCCCCCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAG                         AGCCCTGAAAACTCGAGGGAACCCCCCAAAGTATGGGCTTATATTCCCCTC
genomic: TGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTC

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), 49 (downstream exon)
Score: 701

TTGGAGCTCGCCTAATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTCCTCCTTTATTGGCCGTGCTTCAACTAAGAACAAGGGCAGAATGGCTCGT


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

TTGGAGCTCGCCTAATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTCCTCCTTTATTGGCCGTGCTTCAACTAAGAACAAGGGCAGAATGGCTCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

TTGGAGCTCGCCTAATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTCCTCCTTTATTGGCCGTGCTTCAACTAAGAACAAGGGCAGAATGGCTCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

TTGGAGCTCGCCTAATCTCTCATGCTGGCAGTCTTTCAAACCTTGCTAAGTGTGCAGCCTCCACCCTTCAAATACTTGGTGCTGAGAAGGCCCTATTCAGgttggtaaat ... tgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTCCTCCTTTATTGGCCGTGCTTCAACTAAGAACAAGGGCAGAATGGCTCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagtaagtcttgctagtaggaagatgcccttacacttgtcctttgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTCCTCCTTTATTGGCCGTGCTTCAACTAAGAACAAGGGCAGAATGGCTCGT
                            cccttac  putative branch site (score: 230)
                                    cttgtcctttgtcc  CT-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtaaattcttaaaacatcttttgggtttcccactgtttcaatagttctcagttaactctgtaatttatggttatacactggtcatacttgagtaagtcttgctagtaggaagatgcccttacacttgtcctttgtccaccagAGCACTGAAAACTCGAGGGAACACACCAAAGTATGGGCTTATATTCCACTCCTCCTTTATTGGCCGTGCTTCAACTAAGAACAAGGGCAGAATGGCTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC