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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatacaaacccttccaaatattgtcccttttgtaaagttgtatgcttattataatcagatgctgattaaacacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG

Basic information

species Arabidopsis thaliana
transcript AT5G05780.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G368908_T03 (Zea mays), 3'ss of exon 1
gtaagatacaaacccttccaaatattgtcccttttgtaaagttgtatgcttattataatcagatgctgattaa-acacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
                     || |        |   |   | |  || ||    |  |       || |||| |   || ||   ||  |||||||||||| |||||||| ||||| || || || |||||  || ||||||||||||||||||||||||||||||| |
-------------------gtatgtctgggggatgagatgctggagtgtttcacttgcttgctcagtgtttaatatttttgttgcccttcccagAATGCTACACAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCTGCTCATGAAGTTGAGGAAATTG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 4
gtaagatacaaacccttccaaatattgtcccttttgtaaagttgtatgcttattataatcagatgctgattaaacacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
                | || |  |||     ||  |  |||| |   |||  | |  ||||    | |||       | |||| || | |||||||| ||||||||||| ||||| || || || |||||  || |||||||||| |||||||||||||||||||| |
---------------gtacataacttgctgagttgctggagtttttcacttgct-tgctcagtgtttaatttg-----ttttttcctttacagAATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------gtaagatacaaacccttccaaatattgtcccttttgtaaagtt---gtatgcttatta-taatcagatgct------gattaa---acacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
                                                              |   | |  || ||| |   || |  |           || |   || |||| |  | |||     | ||       | |||   | | ||  || |   | |||||||| ||||| ||||| || ||||| || || |||||| |  |||| |||||||||||||||||||||||||| |
gtacaaattaagtccgtcatatctttgatagaaatcttatatatctgttcttgctgatattttgcaaaagtaatcctgctgtatgtgatggtgggacgggagctagtgtttgctcaacactaaattagtactcaaagaaactaatatatagtttattctgagtacagAATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G03360.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------gtaagatacaaacccttccaaatattgtcccttttgtaaagtt---gtatgcttattat--aatcag-atgctgattaa-------acacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
                                                               |   | |  || ||| |   || |  |       |   || |   || |||| |  |   ||| || || |  |  ||       | | ||  || | | | |||||||| ||||| ||||| || || || || || |||||| |  |||| ||||||||||||||||||||||||||  
ggtacaaattaagtccttcatatctttgatagaattcttatatttctgttcttgctgttattttgcaaaagtaatcctgctgcatgtgatagtgggaggggagctagtgtttgctcaacactaaattagtattcaaaggaactgacatatagtttattctgtgtacaGAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATA-

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------gtaagatacaaacccttccaaatattgtc--ccttttgta-aagttgtatgcttattataatcagatg--ctgattaaacacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
                                                        || | ||   |  |      ||| |||    | |  |||  |||   | |  |||  || |   | ||   |  |  ||  |||  || |   | ||||||||||| |||||||||||||| ||||| || |||||  |  | ||||||||||||||||||||||||||||| |
gtaagaactaagaacatctttaatgttttcttatttagctggtgcatgattgatcagttacattttattcagcttgaatcttgctgacttactgtctaagacatttcattaaaatgacttgttggtttactctaatgcttgcttatggttacagAATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATTGCTGCTCATGAAGTTGAGGAAATTG

upper sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------------gtaagatacaaacccttccaaatattgtcccttt----tgtaaagttgtatgcttattataatcagatgctgatta-aacacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
                                                      || | ||   | |       ||||| | |  |||    | |||     |   || ||  || | ||  | | | |  ||  |||  || |   | |||||||| ||||||||||||||||||||||| || ||  |  || | ||||||||||||||||||||||||||||| |
gtacaactaagaatatcataatgttttttcatttagctggtgcatgattgatcagttacatcataccaagcttgaatatggccagtttactgtttaagaagctccactgatattacttagtggtttactctaatgcttgcttatggttacagAATGCCACTCAGAAAAGCCAGAAAGTTTTTGTCCACATACCTTCTGAAATTGCTGCTCATGAAGTTGAGGAAATTG

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|124918122|gb|EH991990.1|EH991990
EST:     TGGAGGAGGTTAAGGAG                         AATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATT
genomic: TGGAGGAGGTTAAGGAGgtaagataca ... ttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATT
EST: gi|125208644|gb|EL223598.1|EL223598
EST:     AACTTGGAATCCCTACCAAAGCATACTATGCAGTGGGGGAGGTTAAGGAG                         AATGCTACTCAGAAAAGCCAGAAAGTTTTCG
genomic: AACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAGGTTAAGGAGgtaagataca ... ttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCG
EST: gi|47831858|gb|CK121542.1|CK121542
EST:     AACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAGGTTAAGGAG                         AATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATT
genomic: AACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAGGTTAAGGAGgtaagataca ... ttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttgtatgcttattataatcagatgctgattaaacacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG
                         tgctgat  putative branch site (score: 3)
                                    cacttctttttctctc  putative PPT
      tatgcttattataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatacaaacccttccaaatattgtcccttttgtaaagttgtatgcttattataatcagatgctgattaaacacttctttttctctccagAATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT