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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatgattggcaaaccaatctagggatgataaaagtaactaaatctacagcgtgctttccagttcttactttttttagttagaaattttgatctaacattcagaactgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA

Basic information

species Arabidopsis thaliana
transcript AT3G60190.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g41820.2 (Oryza sativa), 3'ss of exon 8
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatgattggcaaaccaatctagggatgataaaagtaactaaatctacagcgtgctttccagttcttactttttttagttagaaattttgatctaacattcagaactgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
                                                                                                      |||  |   |||  |      |     ||    | |||   |  |   ||||||| |||   |    | |  || |   || | ||||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||| || || ||||||||||||||||| ||||||||| | ||||||||  |||| |
------------------------------------------------------------------------------------------------------gtatgtttctctttactactttactttgtatgcaatttgggttat-gtaaattttaatcctcc--caatatttgttcttctcattaagGTTCTCGAAGGAAGATCGTACAGACTGCAGCATCCATGGGTCGGGATTGTTAATCGTTCACAAGCAGATATCAATAAGAATATTGATATGATTATTGCCA

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os09g39960.1 (Oryza sativa), 3'ss of exon 8
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaa--tgattatacatgactggtattatgattggcaaac-caatctagggatgataaaagtaactaaatc-tacagcgtgctttccagttcttactttttttag--ttagaaattttgatctaacattcagaactgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
              ||    ||    |    || | ||    ||  ||   ||  |  ||||     || | |  ||    | |  ||  ||     || |   | |    | ||| |||  |   | |  || || |   |   ||||   ||      | ||  ||| |      |  | | |  |     ||||||||||| |||||| | ||  | || ||  |||| |||||||| || || ||||| ||||||||||||||||| | ||| || ||||||||  ||||||
--------------gtaagattgaacttgcctgccctgacaaacagtagtctgtctgcacattgtcagtttcagaatatctacatgcagcctttttttgttcttaatgttcatatcatacctctgacctgtcatttatctgtaaatttaaccttgttctatctggactacctcgactattttcatttcccccaaagGTTCTTGAGGGAAGAGCCTATCGTCTTCAGTATCCGTGGGTTGGAATTGTCAACCGCTCACAAGCAGATATTAACAGGAAAGTTGATATGATTGTTGCAA

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G070899_T01 (Zea mays), 3'ss of exon 8
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatgattggcaaaccaatctagggatgataaaagtaacta-aatctacagcgtgctttccagttcttactttttttagttagaaattttgatctaacattcagaactgcttgcctt--aataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
                                                                                                    | ||  ||    |||   |    || |    || ||  |||| ||          | ||   |||  | |    || |||   ||  ||| ||||||||||||||||| ||||||| ||||| ||||| |||||||| || ||||||||||||||||||||||| || |||||||| || |||||  |||| |
--------------------------------------------------------------------------------------------------gtatgtgtctgtggtctcttgttctctgtgacttttttgtttttattgccattgggctctg---taatttcccctgcttctttatttccaattagGTTCTTGAAGGAAGAGCTTACAGACTGCAGCATCCCTGGGTTGGAATTGTGAACCGTTCACAAGCAGATATCAACAAGAATGTTGACATGATTATTGCTA

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G055883_T02 (Zea mays), 3'ss of exon 6
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatgattggcaaaccaatctagggatgataa--aagtaactaaatctacagcgtgctttccagttcttactttttttagttagaaatt-ttgatctaacattcagaa--ctgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
                                   | | |  | ||||    |  |     ||| | |||  | ||   |||  ||| |   | |  | |         |   | || |  |||  || | |   |  ||    ||| | |   ||| | |||||| | |  |      || |  ||    | |||||||||| |||||| | ||  |||||||  ||||||||||||| || || || || ||||||||||||||||||| ||| || || |||||    || |
---------------------------------gtaagattgattttatctgtcttctccaacttgaatttcggttactaaaaaaatatgaagttacttatctgtcttgtttgtttatattgtggatttctgacatctctaaggttaatgattgattgtcgatctaccttaaatgttcttgttcccccctcttagGTTCTTGAGGGAAGAGCCTATCGGCTGCAGAATCCTTGGGTTGGAATCGTCAATCGCTCACAAGCAGATATTAATAGGAAGGTTGACATGATTTCAGCGA

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G12850.1 (Glycine max), 3'ss of exon 8
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatgattggcaaaccaatctagggatgataaaagtaactaaatctacagcgtgctttccagttcttactttttttagttagaaattttgatctaacattcagaactgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
                                                                    | ||  ||  ||  ||     |    |       | |  |   | |     |||| |      | | ||  | | || ||||    ||||   || |  |    | | | |       |||||| |||||||||||||||||| | ||||||||||| ||||||||  |||| || || || ||||||||||| ||||| || || ||||||||  |||| |
-------------------------------------------------------------------gtaatatttctcactccctctcacattttccccctgcag-tggttatgagcagtgcctg-----tataaccatatataattag----tttgtcttacccatttttattccct-------taagGTCCTTGAAGGAAGATCTTACCGTCTGCAACATCCCTGGGTTGGTGTAGTTAATCGATCCCAAGCAGATATCAATAAAAACGTTGATATGATTGTTGCTA

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G45380.1 (Glycine max), 3'ss of exon 8
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatgattggcaaaccaatctagggatgataaaagtaactaaatctacagcgtgctttccagttcttactttttttagttagaaattttgatctaacattcagaactgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
                                                           | |      |||   ||    ||   ||  | | |   | || |||| |   | |  || |||| |   |  |  ||||  |||        |   |   |||  | || |       || ||| ||   ||| ||||||||||| |||||  | |||||||||||||||||||| ||||| || || || ||||| || || ||||  ||||| ||||||||  |||| |
----------------------------------------------------------gtaatcttccttac--tttcttaattgatgcatgtacctttaatgtaaatg--tttgaagtgtgcctgtaaaattatactgcttt--------atcctctttctcgctttta-------ttccctcaa---gGTCCTTGAAGGAAGGTCTTATCGCCTGCAACATCCTTGGGTTGGTATAGTAAATCGATCCCAAGCGGACATCAATAGAAATGTTGATATGATTGTTGCTA

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G24610.1 (Glycine max), 3'ss of exon 8
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatg-attggcaaaccaatctagggatgataaaagtaactaaatctacagcgtgctttccagttcttactttttttagttagaaattttgatctaacattcagaactgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
                                    |  |   ||   |   |   ||||      | |  || | |||  |    || ||    | |||||  |   ||| | |     |||| |      | | ||  | | || ||||    ||||   || |  |    | | | |       |||||| |||||||||||||||||| | ||||||||||| ||||| ||  |||| || || || ||||| ||||| ||||| || || || |||||  |||| |
-----------------------------------gtaattttctcacaccctctcacattttccctgtcttgcagtggttatgatatatatacct-ataaagttctataactttgagcagtgcctg-----tataaccatatataattag----tttgtcttacccatttttattccct-------taagGTCCTTGAAGGAAGATCTTACCGTCTGCAACATCCCTGGGTCGGTGTAGTAAATCGATCCCAAGCGGATATCAATAAAAACGTTGACATGATTGTTGCTA

upper sequence: AT3G60190.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv15s0021g00480.t01 (Vitis vinifera), 3'ss of exon 8
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatgattggcaaaccaatctagggatgataaaagtaactaaatctacagcgtgctttccagttcttactttttttagttagaaattttgat--ctaacattcagaactgcttgccttaat-aagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
           |  |||||| |   ||  | ||| |||    |||||  || ||| |  |   || | |  |  ||  | |  ||  ||    |  |||     || ||  |||| | | |    |    | |  |      |  ||  |||||||||||  ||    |||   ||  |||   |   | |||||||||||||||||||| ||  |||||||||||||||||||||| || ||||| || |||||||| ||||| ||||| ||||| || |||||  ||||||
----------gtgagtctctctctctttctctgt-atgtgaaacttttttggttacatgtt-ttgttgtggtctttttctattcatgctgattac-atattgaaaagtatttctaaatcatatggtttcctgccaaacaagat--gtctgaaattttgattgctcttcttcctcacctcttttttgcttgaagGTTCTTGAAGGAAGATCCTATCGGCTGCAACATCCTTGGGTTGGAATTGTGAATCGCTCACAAGCTGATATCAATAAAAATGTGGACATGATTGTTGCAA

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|163996814|gb|ES062330.1|ES062330
EST:     GTGTTCTTACCAAGTTAGACTTGATGGACAAAGGAACTAATGCGTTAGAA                         GTTCTTGAAGGAAGATCTTACAGGCTGCAACA
genomic: GTGTTCTTACCAAGTTAGACTTGATGGACAAAGGAACTAATGCGTTAGAAgtaagcacct ... ccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACA
EST: gi|125234081|gb|EL248166.1|EL248166
EST:     ATGCGTTAGAA                         GTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTG
genomic: ATGCGTTAGAAgtaagcacct ... ccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttttttagttagaaattttgatctaacattcagaactgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA
                       atctaac  putative branch site (score: 2)
                                         cttgcctt  putative PPT
     ttttagttagaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacctcttcgtctcttttggttcatgtgtcatggtccactttaatgattatacatgactggtattatgattggcaaaccaatctagggatgataaaagtaactaaatctacagcgtgctttccagttcttactttttttagttagaaattttgatctaacattcagaactgcttgccttaataagGTTCTTGAAGGAAGATCTTACAGGCTGCAACATCCTTGGGTTGGGATAGTGAACCGTTCACAAGCAGATATTAATAAGAATGTCGATATGATGCTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT