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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatccttgttgtgtatttgtctatttgatttgttcaaaatcgagcgtctgcaaccagatgtttttctgagatgttctattgatggactgcctttgactaattgtttgaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA

Basic information

species Zea mays
transcript GRMZM2G022019_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022019_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g32970.1 (Oryza sativa), 3'ss of exon 2
------------gtacatccttgttgtgtatttgtcta----tttgatttgttcaaaatcgagcgtctgcaaccagatgtttttctgagatgttctattgatggactgcctttgactaattgtttgaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA
              | ||| ||| |  || || |||      | |||  || |    ||  | | ||||   |  ||  | | |   | |  ||||||      | | |   |||| || | || |||||||||| |||||||||| ||||| ||||||||||||||||  ||||| ||||||||| ||||||||||||||||    |||||||| ||||| ||||| |||||||
gtacatttcctctaaaatcattgcttagt-ttggtcggaggctctgaagtgctttggatataacatctgttgcttgacctatcttctaaagtttctatc-----atttctgctgacaaacttttcgaacatgcagCTGATGGCTCTGATTGGAGAGCAGTTTGATGAAAGTGAGGAAATTTGTGGAGTTGTTGCTAGTGTCCGCCAGAGAGGAGACAAGCTTGCATTGTGGACTA

upper sequence: GRMZM2G022019_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G35620.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacatccttgttgtgtatttgtctatttgatttgttcaaaatcgagcgtctgcaaccagatgtttttctgagatgttctattgatggactgcctttgactaattgtttgaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCA------AGAGGAGATAAGCTGGCATTATGGACTA
               |||||     |||  |    |  ||     | | | | |       ||||||  | ||||| | | | | |    || ||    ||| || ||   | ||| ||||||||||| | ||||| ||||| ||||||||| |||| || ||||||||  | ||||||||||||||| ||      |    ||| |||||  | || |      
---------------gtatt---acattctaaccct--aaccctaaccttttactcttctgtgttttgtt-agatgatatgtggttttggtgactggttctatttcttatgatatgtagTTGATGGCTTTGATTGGAGAGCAATTTGATGAAGCAGATGAGATTTGTGGTGTGGTTGCTAGTGTCCGTCCACAGTCGAAGCAAGACAAGCTCTCCTTGT------
















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|18169348|gb|BM339188.1|BM339188
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|87157574|gb|DY402363.1|DY402363
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|211334027|gb|FL370162.1|FL370162
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTCGATGAAACAGAG
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAG
EST: gi|26558254|gb|CA830489.1|CA830489
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|17931601|gb|BM268561.1|BM268561
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|50336177|gb|CO531303.1|CO531303
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|21987193|gb|BQ778721.1|BQ778721
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|211515995|gb|FL388516.1|FL388516
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATCGGGGAGCAGTTCGATGAAACAGAGGACATTTGTGTA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|211062307|gb|FL474478.1|FL474478
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTCGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|18163629|gb|BM333468.1|BM333468
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|4887347|gb|AI677446.1|AI677446
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|211151625|gb|FL390476.1|FL390476
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTCGNTGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|50322671|gb|CO517797.1|CO517797
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|76010904|gb|DT938074.1|DT938074
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|78026174|gb|DV494561.1|DV494561
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|71437159|gb|DR818209.1|DR818209
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|76010903|gb|DT938073.1|DT938073
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|50322672|gb|CO517798.1|CO517798
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|32164823|gb|CD670141.1|CD670141
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|71758459|gb|DR956396.1|DR956396
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|18168337|gb|BM338177.1|BM338177
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|31558353|gb|CD527565.1|CD527565
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|211406227|gb|FL424174.1|FL424174
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTSTTATTGGGGAGCAGTTCGATGAAACAGAGGACA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACA
EST: gi|32933632|gb|CF038444.1|CF038444
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATCGGGGAGCAGTTCGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|16925812|gb|BM078880.1|BM078880
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|22935572|gb|BU571847.1|BU571847
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|91049925|gb|EB160343.1|EB160343
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGA
EST: gi|211020161|gb|FL408602.1|FL408602
EST:     CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACG                         TTGATGGCTCTTATTGGGGGAGCAGTT
genomic: CTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGG-AGCAGTT

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: 260

AGTAGAGCCAAAATGGGAAGACCCAGAGTGTGCAAATGGTGGCAAATGGACTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 303

AGTAGAGCCAAAATGGGAAGACCCAGAGTGTGCAAATGGTGGCAAATGGACTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 399

AGTAGAGCCAAAATGGGAAGACCCAGAGTGTGCAAATGGTGGCAAATGGACTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 215

AGTAGAGCCAAAATGGGAAGACCCAGAGTGTGCAAATGGTGGCAAATGGACTGTCCCATGCAACAGAAAGGCAACCTTTGAGACCATGTGGCTTGAAACGgtacatcctt ... gaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgagatgttctattgatggactgcctttgactaattgtttgaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA
                                 gactaat  putative branch site (score: 215)
                                    taattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatccttgttgtgtatttgtctatttgatttgttcaaaatcgagcgtctgcaaccagatgtttttctgagatgttctattgatggactgcctttgactaattgtttgaacatgcagTTGATGGCTCTTATTGGGGAGCAGTTTGATGAAACAGAGGACATTTGTGGAATTGTTGCTAGTGTCCGTGCAAGAGGAGATAAGCTGGCATTATGGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG