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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagggagcgcgtgtttaaatttttccatatcctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGGTGGGAATTTAACATGTTCTCTGTAATACTGTGAATCTGTTGCT

Basic information

species Zea mays
transcript GRMZM2G128171_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 3
gtgagggagcgcg-----tgtttaaatttttccatat-cctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGGTGGGAATTTAACATGTTCTCTGTAATACTGTGAATCTGTTGCT
||||||  ||        |||| ||||  ||    |   ||        |||  | |     |  |||   | ||  ||    | |  |||||||||||||||||||| |||||| ||||||||||||||| | || ||||||||||                                            
gtgaggctgcataacttttgttcaaatacttttgaacatctacaccagacaaaattt-----tcatgatttatatcactacaaccatgtagGTATGAAGGACAACGCAGTGCAGAGGCCCTTGCTGAATTTGTTAACACTGAAGGAG--------------------------------------------
















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|211249331|gb|FL145209.1|FL145209
EST:     GGGTATCNAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTWGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211249326|gb|FL145204.1|FL145204
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACA
EST: gi|211249337|gb|FL145215.1|FL145215
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACT
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACT
EST: gi|211251557|gb|FL145220.1|FL145220
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211242633|gb|FL145173.1|FL145173
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCC
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCC
EST: gi|211247093|gb|FL145191.1|FL145191
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAA
EST: gi|211242629|gb|FL145169.1|FL145169
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGGAAGCCCTTGCTGAATTTCTCAATACTG
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAG-AAGCCCTTGCTGAATTTCTCAATACTG
EST: gi|211244868|gb|FL145188.1|FL145188
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCT
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCT
EST: gi|78117464|gb|DV535851.1|DV535851
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211244858|gb|FL145178.1|FL145178
EST:     GGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCC-AAAATA                         GTATGAAGGACAACGCACTGCA
genomic: GGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAA-Agtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCA
EST: gi|211247098|gb|FL145196.1|FL145196
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGC
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGC
EST: gi|211249329|gb|FL145207.1|FL145207
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCNGAATTTCTCAATACTGA
genomic: GG-TATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211249334|gb|FL145212.1|FL145212
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
EST: gi|211251558|gb|FL145221.1|FL145221
EST:     GTATCCAACAATCCAATGGTTCCCGGAAAGGATCCTTGGAGCCCCAAAAA                         GTATGAAGGACAACGCACTGCAG
genomic: GTATCCAACAATCCAATGGTTCCCG-AAAGGATCCTTGGAGCCC-AAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAG
EST: gi|211249328|gb|FL145206.1|FL145206
EST:     GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAA                         GTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA
genomic: GGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGA

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), 46 (downstream exon)
Score: 169

GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGGTGGGAATTTAACATGTTCTCTGTAATACTGTGAATCTGTTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGGTGGGAATTTAACATGTTCTCTGTAATACTGTGAATCTGTTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 423

GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGGTGGGAATTTAACATGTTCTCTGTAATACTGTGAATCTGTTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 555

GTTGATTGTGATGAGCACAAGAGTTTGTGCAGCAAGTATGGAGTTTCCGGGTATCCAACAATCCAATGGTTCCCGAAAGGATCCTTGGAGCCCAAAAAgtgagggagc ... ggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGGTGGGAATTTAACATGTTCTCTGTAATACTGTGAATCTGTTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGGTGGGAATTTAACATGTTCTCTGTAATACTGTGAATCTGTTGCT
                          ttctgac  putative branch site (score: 555)
                                      ttcctttg  putative PPT
                                                aaatta  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagggagcgcgtgtttaaatttttccatatcctttgtttaccaagttctgtgaattctgacagaaattcctttggcaaattagGTATGAAGGACAACGCACTGCAGAAGCCCTTGCTGAATTTCTCAATACTGAAGGAGGTGGGAATTTAACATGTTCTCTGTAATACTGTGAATCTGTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG