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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttttattttgaacaagcaaagcttcctggttcccttgtttacgtttggggttctataatttgctgaattgttgctataatatatatttttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG

Basic information

species Zea mays
transcript GRMZM2G032699_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032699_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g22950.3 (Oryza sativa), 3'ss of exon 1
atcttttatt--ttgaacaagcaaagcttcctggttcccttgtttacgtttggggttctataatttgctgaattgttgctataatatatatttttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG
 |   | |||  |||  | | |   ||    || ||   |||  |   | |    |||| |  || | |  | |    ||  |||   |  ||||    ||||| ||||| |||||||||||| |||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||
gtacatgattggttgttccaactttgcaaattgcttaagttggctgtatatcat-ttcttttgttggttagaattgcactg-aatggttccttttttgacagGTTTGCGATGAGCTTGAGGACGTGATGGAAGAAGGTGGTATACTAGTAGATTACCATGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTTGTAGTTG

upper sequence: GRMZM2G032699_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g22950.2 (Oryza sativa), 3'ss of exon 2
atcttttattttgaacaagcaaagcttcctggttcccttgtttacgtttggggttctataatttgctgaattgttgctataatatatatttttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG----------------------------------------------
                                                                                                                                      |||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||| |||||||                                              
--------------------------------------------------------------------------------------------------------------------------------------gtggtatactagtagattaccatggatgtgatttctttccagaacgttggtttgaccttgtagttgtgctccaaacagATAACTCAATTCTGCATGATCGCTTGACTAGCAG

upper sequence: GRMZM2G032699_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g22950.2 (Oryza sativa), 3'ss of exon 1
atcttttatt--ttgaacaagcaaagcttcctggttcccttgtttacgtttggggttctataatttgctgaattgttgctataatatatatttttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG
 |   | |||  |||  | | |   ||    || ||   |||  |   | |    |||| |  || | |  | |    ||  |||   |  ||||    ||||| ||||| |||||||||||| ||||||||||||                                                                  
gtacatgattggttgttccaactttgcaaattgcttaagttggctgtatatcat-ttcttttgttggttagaattgcactg-aatggttccttttttgacagGTTTGCGATGAGCTTGAGGACGTGATGGAAGAAG------------------------------------------------------------------

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|60341109|gb|DN208082.1|DN208082
EST:     ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTG                         GTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
genomic: ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
EST: gi|211455241|gb|FK989201.1|FK989201
EST:     ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTG                         GTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGTATACTAGTAGAT
genomic: ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
EST: gi|6695878|gb|AW288986.1|AW288986
EST:     ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTG                         GTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGTATACTAGTAGAT
genomic: ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
EST: gi|60359354|gb|DN226327.1|DN226327
EST:     ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTG                         GTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGTATACTAGTAGAT
genomic: ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
EST: gi|5525640|gb|AI861533.1|AI861533
EST:     ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTG                         GTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGTATACTAGTAGAT
genomic: ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
EST: gi|6194875|gb|AW146979.1|AW146979
EST:     CAACGAGGACCTG                         GTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGTATACTAGTAGAT
genomic: CAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
EST: gi|60358371|gb|DN225344.1|DN225344
EST:     ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTG                         GTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
genomic: ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT
EST: gi|37387580|gb|CF630987.1|CF630987
EST:     ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTG                         GTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGTATACTAGTAGAT
genomic: ACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGAT

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: 159

AGGCCTCCGCCACGTCAACATCGGCGACCTCGTCCGCGAGAAGAGCCTCCACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

AGGCCTCCGCCACGTCAACATCGGCGACCTCGTCCGCGAGAAGAGCCTCCACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

AGGCCTCCGCCACGTCAACATCGGCGACCTCGTCCGCGAGAAGAGCCTCCACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 56

AGGCCTCCGCCACGTCAACATCGGCGACCTCGTCCGCGAGAAGAGCCTCCACGACGGCTGGGACGCCGACCTCGAGTGCCATGTCATCAACGAGGACCTGgtaagtctcg ... tttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggggttctataatttgctgaattgttgctataatatatatttttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG
                                           tttttgcc  CT-rich tract
                     tgaattgttgctataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttttattttgaacaagcaaagcttcctggttcccttgtttacgtttggggttctataatttgctgaattgttgctataatatatatttttgccgcagGTGTGCGACGAGCTTGAGGACATGATGGAAGAAGGTGGCATACTAGTAGATTACCACGGATGTGATTTCTTTCCAGAACGTTGGTTTGACCTCGTAGTTG

- - - - - - - -caagcaa
- - - - - - - - - - - - -ttcctgg
- - - - - - - - - - - - - - - - - - cttgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct