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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAACCAGAGCCAAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttttagtaatgcttcaatattttttatagaagtttgggcttcccattattgaaatgcttaatgcttgggatactgtttgatcgtaagtactaa...

Basic information

species Zea mays
transcript GRMZM2G039325_T01
intron # 10
splice site 5'
intron type U2

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|16926574|gb|BM079642.1|BM079642
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|16378770|gb|BI992594.1|BI992594
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|14202547|gb|BG836224.1|BG836224
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|211352090|gb|FL449510.1|FL449510
EST:     AGCTGCTTGGT-CGAAAAGGCTCTGGTAGTTCACAACTGCTTCCTGAAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AGCTGCTTGGTACG-AAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|6012204|gb|AW061746.1|AW061746
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|60338105|gb|DN205078.1|DN205078
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|5713754|gb|AI943746.1|AI943746
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCGCAACTGCTTCCTGGAAG                         GAACGCAGCCCGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|29945923|gb|CB815888.1|CB815888
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|71760015|gb|DR957952.1|DR957952
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|14646151|gb|BI180340.1|BI180340
EST:     CTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: CTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|14585543|gb|BI135295.1|BI135295
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCCCGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|211530545|gb|FL066727.1|FL066727
EST:     -GCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCCCAAC
genomic: AGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGC-TTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAAC
EST: gi|14202541|gb|BG836218.1|BG836218
EST:     AGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTCGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACT
genomic: AGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCT-GGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACT
EST: gi|5058732|gb|AI737208.1|AI737208
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|12969360|gb|BG266304.1|BG266304
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|78024888|gb|DV493275.1|DV493275
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|78024574|gb|DV492961.1|DV492961
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
EST: gi|148967768|gb|EE019045.2|EE019045
EST:     AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAG                         GAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA
genomic: AAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTA

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), 47 (downstream exon)
Score: 283

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAACCAGAGCCAAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTAACACGAAGCAGCATTCTTGGATAGATCCTTCTCCGTTCCACCATTTGTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAACCAGAGCCAAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTAACACGAAGCAGCATTCTTGGATAGATCCTTCTCCGTTCCACCATTTGTT


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 29

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAACCAGAGCCAAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTAACACGAAGCAGCATTCTTGGATAGATCCTTCTCCGTTCCACCATTTGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 139

AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAACCAGAGCCAAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttt ... atgcctgcagGAACGCAGCACGAACTGGGTCGATGCGCAACTTCCAGTGATGGCAGCACTAACACGAAGCAGCATTCTTGGATAGATCCTTCTCCGTTCCACCATTTGTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAGAAGTTGCAGCAATGCGTGCCAGTAAAGAACAAGAAACCAGAGCCAAGCTGCTTGGTACGAAAGGCTCTGGTAGTTCACAACTGCTTCCTGGAAGgtacattttttagtaatgcttcaatattttttatagaagtttgggcttcccattattgaaatgcttaatgcttgggatactgtttgatcgtaagtactaa

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG