Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttaatggctcctctcatttttacttttgatctttcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG

Basic information

species Arabidopsis thaliana
transcript AT1G16010.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g44150.1 (Oryza sativa), 3'ss of exon 3
gtactttaatggctcctctcatttttacttttgatctt-tcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
||| |  |    |||  | ||   |  |  || ||||| | ||   |    |||  | |     ||| |  |  || ||   || ||| | ||||||||||||||||||||||||||||| || ||||||||  ||
gtaatgaaccacctctccccaaaatcccaattaatcttgtttttcattactagcagttacaggatgtctgaccttcattttctttcagCTGAAGGAGTACATTGATGACACTGAAGATTTTATCAACATTCAGTTG

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G064467_T01 (Zea mays), 3'ss of exon 3
gtactt-taatggctcctctcatttttacttttgatctttcttcgctagacagctttaat---catctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
||||     |||  |  | |   | |||  |||| |  |  ||  | |||    | |  |   ||  | || | ||| |     ||| ||| |||||||||| ||||||||||| ||||||||||| ||||| ||||||
gtacaaactatgaattgtgtatatgttagctttgtttctgttttac-agattattatggttgacaattttgctactcgcacattttttcagCTAAAGGAGTATATTGATGACACAGAAGATTTCATCAACATACAACTG

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G170326_T02 (Zea mays), 3'ss of exon 3
--------gtactttaatggctcctctcattt----ttacttttgatctttcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
          |  | |   ||   ||| |  |    |||| | | ||  | || |  |||  ||    |    ||||   |  | |   | |||| ||| | || ||||||||||||||||||||||| ||||| |||||||| |||
gtaccaagccatatcaccagcatgtcttaaatctggttacgtataataatactgcaatagg-agtcaaaggggtctgatctatttttacttcttt-cagCTTAAAGAGTACATTGATGACACTGAAGACTTCATCAACATTCAGCTG

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G108477_T01 (Zea mays), 3'ss of exon 3
---------------------gtactttaa---tggctcctctcatttttacttttgatctt-tcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
                      ||  ||||   |||||   || || | || |  | || |  |    |  | |  | | | || |||||| || |  |||||      ||| | || |||||||| |||||||||||||| ||||| |||||||| |||
gtaccgagccatatctccagcatatcttaaatctggctatgct-atgtgtagtaataatgtgataggagtgaaaggggtctgatgatctgtttttccttcttt------cagCTTAAAGAGTACATCGATGACACTGAAGACTTCATCAACATTCAGCTG

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G00510.1 (Glycine max), 3'ss of exon 4
gtactttaatggctcctctcatttttacttttgatctttcttc--gctagacagc--tttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
         |     || | || |  |||     | || ||||  |||  | | |  ||||   | |  |||| |   ||||   || ||||| || || |||||||||||||| ||||||||||| ||||||||||||
--------gtaaacactgttatctacactaacccttttccttctggcttcataacagtttagcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACCGAAGATTTCATCAACATTCAACTG

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G44820.1 (Glycine max), 3'ss of exon 4
gtactttaatggctcctctcatttttacttttgatctttcttcgctagacagc--tttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
|||     || |        |   | ||| ||  || ||  | |||  | | |  ||||   | |  |||| |   ||||   || ||||| || || |||||||||||||| ||||||||||| ||||||||||||
gtaaac--atagtgttatctacactaactctt--tcctttctggcttcataacagtttatcaaccactgtttcctgctttttgtttcagTTGAAAGAATACATTGATGACACAGAAGATTTCATCAACATTCAACTG

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0018g00600.t01 (Vitis vinifera), 3'ss of exon 3
gtacttta-atggctcctctcattttta---------cttttgatctttcttcgctagacagctttaatcatctgtgttcctctcttta---ctttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
|||   |  ||   || |  ||||| ||         ||||| || |   |  | | |   |    ||   | |  |||  | |||| |   | || ||| | ||||| |||||||||||||| |||||||||||||||||||| |||
gtatcctgcatctttctttacatttgtagacccttgtcttttaatatacttcaggtggggtggagaaaatttattagttagtttcttcatgtcgtttcagCTGAAGGAATACATTGATGACACAGAAGATTTCATTAACATTCAGCTG

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ18545 (Selaginella moellendorffii), 3'ss of exon 4
gtactttaatggctcctctcatttttacttttgatctttcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
|||     | || | |    |||||    |   |         ||| |   |  |||  | | |   |  | ||  ||| |  |||| | |||||||||||||| ||||| || |||||||| ||||| ||||||
gtaaggcgaaggtttcgag-attttcgagtgaaaaaaagaaaggctcg-tggtgttatccgtgttaatctcgctggtta-tacacagCTCAAGGAGTACATTGACGACACCGAGGATTTCATCAACATCCAACTG

upper sequence: AT1G16010.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ36513 (Selaginella moellendorffii), 3'ss of exon 4
gtactttaatggctcctctcatttttacttttgatctttcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
|||     | || |  ||   |||||    |  |         |       |  |||  | | |   |  | ||  ||| |  |||| | |||||||||||||| ||||| || |||||||| ||||| ||||||
gtaaggcgaaggtt--tcgagtttttcgagtgaaaaaaagaaaggctcgtggtgttatccgtgttaatctcgctggtta-tacacagCTCAAGGAGTACATTGACGACACCGAGGATTTCATCAACATCCAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctttcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG
                    ctttaat  putative branch site (score: 4)
                             tctgtgttcctctctt  putative PPT
                     tttaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttaatggctcctctcatttttacttttgatctttcttcgctagacagctttaatcatctgtgttcctctctttactttacagTTAAAGGAGTACATTGATGACACTGAAGATTTCATTAACATTCAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA