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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagatgttttactgttatgattgctaacaatgttttgtaacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

Basic information

species Arabidopsis thaliana
transcript AT1G79990.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
gtaagcagatgttttactgttatgattgctaac--aatgttttgt----aacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
         ||||||  || ||  | |||   |  | ||| | ||    || |     |||    | |    ||| |  || |||||| || || ||||| |||||| | |||||||||||||||||||| |||||||||||||| ||| | ||||  || |||||  | ||||| || || || 
------gtgtgttttcttgataatactgcctgcttattgtctggtgttgaattcttgaactaacatatt---tttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
gtaagcagatgttttactgttatgattgctaacaatgttttgtaac-----ttactgacttctgtgtccactttatgat-----tacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
          | |||      |  | || |  |  | |||||||||      |  | | ||||||| | |   ||| |      |||||| | ||||| ||||| |||||| | |||||||||||||||||||| |||||||||||||| ||||||||||| || |||||| | ||| | || || || 
------gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataagcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
gtaagcagatgttttactgttatgattgctaacaatgttttgta--acttactgacttctgtgtccactttatgatt----acagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
        |||||||   |  |  | ||||  |  |  ||||||  |  |  | | |||| || | |    ||   |    ||||||| ||||| ||||| |||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || ||  || | ||| | || || || 
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
gtaagcagatgttttactgttatgattgctaacaatgttttgta--acttactgacttctgtgtccactttatgatt----acagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
        |||||||   |  |  | ||||  |  |  ||||||  |  |  | | |||| || | |    ||   |    ||||||| ||||| ||||| |||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || ||  || | ||| | || || |||
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 5
gtaagcagatgttttactgttatgattgctaacaatgttttgta--acttactgacttctgtgtccactttatgatt----acagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
        |||||||   |  |  | ||||  |  |  ||||||  |  || | | |||| || | |    ||   |    ||||||| ||||| ||||| |||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || ||  || | ||| | || || || 
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctattaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
gtaagcag-atgttttactgttatgattgctaacaatgttttgtaacttactgacttctg-tgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
|||||||| |||    |    ||    || |     |   |  |   ||  ||  || ||    | | ||| | ||||||||||  | || || ||||||||  | ||||||||||||||||| || |||||||||||||| ||||||||||| || |||    | ||||| || || || 
gtaagcagcatgcagcatacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatttttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtaagcagatgttttactgttatgattgctaacaatgttttgtaacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
|||||  |||   |   |   || |||   || |      || |     |    || | | |  ||| | | | | ||||||||| ||||||||  ||||||||||||||||||| |||||||| ||||| |||||||| |||||||||  ||| |||||| |  |||| |||||||||
gtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttact-cagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
gtaagcagatgttttactgttatgattgctaacaatgttttgtaa----cttactgacttctgtgtccac---tttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
|||||   |  || | ||   || |||   |    |   ||| ||    |||    | || | |||  |    ||  |  |  ||||||||| ||||||||  | |||||||| ||||||||||||||||| |||||||||||||| |||||||||  ||| |||||  |  | || ||||| || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctgtttatcaattgtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
gtaagcagatgttttactgttatgattgctaacaatgttttgtaa----cttactgacttctgtgtccac---tttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
|||||   |  || | ||   || |||   |    |   ||| |     |||    |||| | |||  |    ||| |  |  ||||||||| ||||||||  | |||||||| ||||||||||||||||| |||||||||||||| |||||||||  ||| |||||| |  |||| ||||| || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgtttatcaattttttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 5
gtaagcagatgttttactgttatgattg-----ctaacaatgttttg----taacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
|||||  |||   |   |   || |||      ||  |||||   ||    | | ||  |  ||||| | |  ||| | | | | ||||||| | ||||||||  ||||||||||||||||||| |||||||| || || ||||| || |||||||||  ||| |||||| |  |||| |||||||||
gtaagtggatcaatggtttgcattattcaaaatctctcaatgcagtggtcctgattttttttcttcttttttaactgtgttact-cagTGTTGTGGGATACACACTACTTTTAAGTTTGATTGAATACAAGACACTAGTCATGCGCGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
gtaagcagatgttttactgttatgattgcta-acaatgttttgtaacttactgacttctgtgtc-------------cactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
|| ||  ||  |||  | |  | |     |  |   || ||  |   || || || ||| | |                | || | | | |||||| || |||||||| |||||| | ||||||||||||||||||||||||||||||||||| ||  |||||| ||| |||||| | |||||||||||||| 
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC

upper sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
----gtaagc--agatgttttactgttatgatt--gctaacaatgtt-ttgtaacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
    |  |||   |  | |  |||  |   ||    ||     |||| |||||| | |   |  | | | |    | | | ||  ||||||||| ||||| || |||||| | | |||||||||||||||||| ||||| ||||||||||| ||  |||  || | |||| | |||||||  ||||||
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttat-gcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctaacaatgttttgtaacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT
                       tactgac  putative branch site (score: 1)
                                          tttatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcagatgttttactgttatgattgctaacaatgttttgtaacttactgacttctgtgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT