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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgtcatattgtggtagctttgtagaatgtaacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC

Basic information

species Arabidopsis thaliana
transcript AT1G47380.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g35910.1 (Oryza sativa), 3'ss of exon 4
aactgtcatattgtggtagctttgtagaatgtaac--acatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatttt---tttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
      | || ||| ||   ||  |||  |    |  | ||  |    | || || | | |     || |    |||| ||   |   |  | || |      ||||||| ||||| ||||| |||||||||||| ||||||| ||||| || |||||||| | |||||| ||  ||| ||||||||| ||||||||||| ||||
-----gcgtactgttgttctttgttagtttactgcttaaatgtgttcctttcctttttctgcttgcttcatttttttttatttttgctttcttttctacccccagATTGGCCCTCTTAGATGCTGGCCTGGTGGTTTGTGTCTATCAAGGTCAATTGGAGACCAGGATGTGGGTCAATTCATTGTTCCGGTTCCTTATGTCAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g28560.1 (Oryza sativa), 3'ss of exon 4
aactgtcatattgtggtagctttgtagaatg--taacacatagggaaatatctttgtgc-cgtcaaattgaagagtttt-gataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
     ||| |||||| |   ||||| |  ||  |  |   |        |||| | ||          || ||  || | || || |     ||   |||  || |||||||||| ||||||||||| |||||||||||  | || ||||| ||||| ||| |||||||||| |||| |||  |||| |||||| |||| || |
----atcaaattgtgttcaatttgttgtgtggttgcctggtcttctttgatctatatgtatactttgctgtagtattctagaaaattgtcatttgcgtttacagGTTGGTCCTCTAAGATGTTGGCCAGGTGGTCTGTGCTTATCTAGATCAATTGGGGATATGGATGTTGGTGAATGCATCATTCCTGTTCCTCATGTGAAAC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g37660.2 (Oryza sativa), 3'ss of exon 4
aactgtcatattgtggtagctttgtagaatgt-----aacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
|  |    |||  ||       ||| || |||         |||||  || | ||  ||    | ||  |   |     ||||    |   |||| |   |  ||||||| || || |||||||||||||||||  |||| || |||||||| ||||| |||| |||||| || ||||  ||  |||| || |||||||| ||||
agttagtttatgttgtacatgctgttgattgttgaaaggttcatagaaaattgtccctg-attgacacctctta----cttgacccttctttcttgtccatacagATTGGGCCACTTAGATGTTGGCCTGGTGGCTTGTGCCTATCAAGATCAATTGGTGATCAGGATGTAGGTGAATTTATCATTCCCGTGCCTTATGTGAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G044382_T01 (Zea mays), 3'ss of exon 4
-aactgtcatattgtggtagctttgtagaatgtaacacatagggaaatatctttgtgccgt-caaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
      || |     |||    || |||| |   |    | ||    ||  | ||  || | |    |   ||   ||  |  ||   | ||||   |  |||||||||| || ||||||||||| |||||| | || ||||||||||| ||||| |||| |||||| || ||||  ||| |||| ||||||||||| ||||
tggacatcttccataggttttcttttagagtcctattttttggtttgtagatgtgatccatgccttcttttgatccttagttcctt--ttttatccatccagATTGGTCCCCTTAGATGTTGGCCAGGTGGTTTATGCCTCTCAAGATCGATTGGTGATCAGGATGTAGGTGAATTTATTATTCCGGTTCCTTATGTGAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G135444_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------aactgtcatattgtggtagctt--tgtagaatgtaaca-catagggaaatatctttgtgccgtcaa----attgaagagttttgat--aactaaat---cttattttttta-------gATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
                                                                 |||  ||  ||||||   | ||   ||| ||  |      ||||     | || ||||   ||       |||  | |   |  ||   | ||||     |||  ||||||       | |||||||||| ||||||||||| |||||| ||||||| || |||||||| || ||||| |||||||| |||| |||  || | |||||| |||| ||||
gttcgtgtctgtctcacccttaaccctgtgcgctcatgaatggattttgtgtgtgtttggcgtataacc-tcccattgtgtgtgtttggcgtataacctcctggtatagtttggtctccttgttttgtttgttctattatataacgtacattggagtaaacaggtttacctttttacatttcagGTTGGTCCTCTAAGATGTTGGCCAGGTGGTTTGTGTCTATCTAGATCCATAGGGGATCTTGATGTTGGTGAATGCATCATTGCTGTTCCTCATGTTAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G015610_T02 (Zea mays), 3'ss of exon 4
aactgtcatattgtggtagctttgtagaatgtaacacatagggaaatatctttgtgccgt-caaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
 ||        |  | |  | || |||| |   |    | ||    ||  | ||   |   |    |   ||   || ||  ||   | ||||   |  |||||||||| || ||||||||||| |||||||| || ||||||||||| ||||| |||| ||| || || ||||  ||  |||| ||||||||||| ||||
gacatcttccataggttttccttttagagtcctatcttttggtttgtaggtgtgattcacaccctcttttgatcctttattccttt-ttttatccatccagATTGGTCCCCTTAGATGTTGGCCAGGTGGTCTATGCCTCTCAAGATCGATTGGTGATCAGGACGTAGGTGAATTTATCATTCCGGTTCCTTATGTGAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G052699_T02 (Zea mays), 3'ss of exon 4
-aactgtcatattgtggtagctttgtagaatgtaacacatagggaa-atatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
  ||  |      ||| | | |||| ||  |     |  |        ||| ||| | |  || | |||       |  |||  ||| | || |   |  ||||||| || || |||||||||||||| ||| |||| || ||||| || ||||||||||  |||||||| ||||  || ||||||||||||  ||| ||||
acaccatgggcaggtgatggttttggagttttggttaattgctctttgtatattttttctttccacttgcttgacct--atatttaatttttttacctccagATTGGCCCCCTTAGATGTTGGCCTGGAGGTTTGTGCCTATCAAGGTCAATTGGAGATCAAGATGTTGGTGAATTTATCGTTCCAGTTCCTCTTGTGAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G081359_T01 (Zea mays), 3'ss of exon 3
-------aactgtcatattgtggtagctttgtagaatgtaacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatt-tttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
       | | | | |||  |  | | ||| | |  |  ||  |     | | | | ||  | ||  |   ||||         |||  ||| |||| ||   |  ||||||||||||| || ||||||||||| ||| |||| || || || || || |||||||  |||||||| ||||  |||||||||||||||  ||| ||||
caccatgagcaggc-tatgattttggattttttggtta-aatgctctttgtagttttttctttccacctgtttga------cctatatgtaattcttcttacctccagATTGGTCCTCTTAGGTGTTGGCCTGGAGGTTTGTGCCTATCTAGGTCAATAGGAGATCAAGATGTTGGTGAATTTATTGTTCCAGTTCCTCTTGTGAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 4
-------aactgtcatattgtggtagctttgtagaatgtaacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
          |    | ||||  |    || |       || |     | |||  | ||| ||     | ||| |   |  |   ||  | ||| |   | |   || |||||||| |||||||||||||||||||| ||||||||||| |||| ||||||||| ||||| |||| ||||  ||||| || || || ||||||||||
acacttttgtttaggttttgtactcatgttttgtttaccaatattattgaaaaagtgtttatg-----atattaatatgcctgactagattaatttg--tatcaaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGTTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTACCTGTCCCGTATGTAAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G04040.1 (Glycine max), 3'ss of exon 4
aactgtc-atattgtggtagctttgtagaatg-taacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatc--ttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
  || |  | ||| |  |  ||||| |   |  ||| |        |  |      |||  |  | ||| |   |     |  ||| ||   | || ||| ||| |||||||| |||||||||||||||||||  ||||||||||| |||||||||| ||| |||||||||| ||||  ||||| || || ||  | |||||||
-gctatttagattatcttc-ctttgcaatttactaatattctctctagaagaaacttgcatttgagttgtattatgcc--tggctagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACACGTAAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G04210.1 (Glycine max), 3'ss of exon 4
aactgtcatattgtggtagctttgtagaatg-taacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatc--ttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
 |   |   ||| |  |  ||||| |   |  ||| |        |  |      |||  |  | ||| |   |     | |||| ||   | || ||| ||| |||||||| |||||||||||||||||||  ||||||||||| |||||||||| ||| |||||||||| ||||  ||||| || || ||  |||||||||
gatatttggattatcatc-ctttgcaatttactaatattctctctagaagaaacttgcatttgagttgtattatgcc--tgactagattaatgatatttgtagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCCATTGGTGATATGGATGTTGGTGAATTTATTGTCCCTGTACCACATGTAAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 5
-------aactgt-catattgtggtagctttgtagaatgtaacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
        ||| | || |   |  | | ||  |      ||     |   ||||  | ||| ||     | | | |   |  |   ||  | ||| ||  | ||  || |||||||| |||||||||||||||||||  ||||||||||| |||| ||||||||| ||||| |||| ||||  ||||| || || || ||||||||||
gattttgtactatacagaccata-tggtttgtttaccaatattctctttagaaaagtgtttatg-----atactaatatgcctgactagattaatttt--tattgaagGTTGGTCCTTTGAGATGTTGGCCTGGTGGCTTGTGTCTCTCACGATCTATTGGAGATATGGATATTGGTGAATTTATTGTCCCTGTACCGTATGTAAAGC

upper sequence: AT1G47380.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 5
aactgtcatattgtggtagctttgtagaatgtaacacatagggaaatatctttg---tgccgtcaaattgaaga--gttttgataacta--aatcttattttttt--agATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
   ||| |  || |          |  ||    |  || | | || | | |  |   ||  || |  || || |  |  |  |||||||  |  || ||| |  |  ||||||||||| ||||||| |||||||||||| |||| || ||  |||||||||| ||| |||||||||| || | ||||||||| ||||||||||||||||
---tgtgactttct------cccatccaaccctattcagatgaaattgtatcaggtttgttgttaggtttaaaacaggctgaataactagtacactaattctcctgcagATTGGTCCTTTGAGATGCTGGCCTGGTGGTTTGTGCCTTTCCCGATCCATTGGTGATATGGATGTTGGAGAGTTCATTGTTCCGGTTCCTTATGTAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC
                                  aactaaa  putative branch site (score: 2)
                                         tcttattttttt  CT-rich tract
                         agttttgataactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgtcatattgtggtagctttgtagaatgtaacacatagggaaatatctttgtgccgtcaaattgaagagttttgataactaaatcttatttttttagATTGGTCCTCTGAGATGTTGGCCTGGTGGTCTGTGTCTCTCAAGATCCATTGGAGATCTGGATGTTGGCGAATACATTGTTCCAGTTCCTTATGTAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - -taacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgtcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaa