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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttgtgacactctctggttttgttccatttaattactggatagattgaatttccaaagctaactttttcttatttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 10
---------------gtaccttgtgacact-ctctggttttgttccatttaattactggata--gattgaatttccaaagctaactttttcttatttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG
               ||    |  |    |  | |   | ||||  |  |||||  |  ||     |   ||     |   |||| | | || |||| |  ||||||| || |||||  |||| || |||||||| |||||||||||||||||||||||||| |||
gtgtatttctcatttgtttactaggcttttgtttttaatatgttggaaataattcttctatctcagtctcatgcattagcataacatctactcatttgc--agTACTCTAATTCTGACACTGTGGTTTATGTTGGATGTGGAGAGAGAGGAAATGAAATGGCAGAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------------gtaccttgtgacactctctggttttgttccatttaattactggatagattgaatttccaaagctaactttttcttatttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG
                                 | | | ||||| | |  |||   | | ||  |  || |   ||  ||    |    |||  |    | | | | |  |   ||||||| || || ||  |||| || ||||||||||||||||| ||||||||||||||||| |||
gtgagcttgtcttttattcacttgggaccagacatcctttgacaatattaggt---gctacaaattctttccttattcatcttgtacttaaatgttgtgtgtacatgtacatgcagTACTCTAATTCAGACACTGTGGTTTATGTTGGTTGTGGAGAAAGAGGAAATGAAATGGCGGAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------gtaccttgtgac----actctctggttttgttccatttaattactggatagattgaatttccaaag--------ctaactttttcttatttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG
                                          |  | || ||       ||| |||||||     || |  || ||| | |  | |  ||   || |        || | ||  |  | ||| |  |||| ||||||||  |||||||||| || ||||||||||||||| | || |||||||||||||||
gtagttggttgcaactgattgaattttttgcatttcatttcatttcatgggatcttagttctgtggtttttacttatgtttttcctgcaaaagtggtgttggtaatgacactcgactcatttaattgtttttgcgcagTATTCCAACTCCAATGCTGTTGTTTACGTTGGTTGTGGAGAGCGTGGGAATGAAATGGCTGAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 10
-----------------------------------------------------gtaccttgtgacactctctggttttgt--tccattt-----aattactggatagatt-------gaatttc-----caaagctaacttttt-----cttatttacat--agTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG
                                                      |  ||| |     ||| ||||| |||  |  |  |     || || ||  |  | |        || |||     | | ||| | |||||      || |||   |  |||||||||||||  |||| ||||| || || || ||||||||| | ||||||||||||||||||
gtagttggttacatctgtttggatttttcgaagttcatttcgcatcatacattttttctttttcttttctttggttgtgtatttaagctgcagaaactattgtttgaagtttgtatgaaagttctggaacgaggcttattttttgcaaatttgtttgtgtgcagTACTCCAACTCCAATGCAGTTGTTTACGTCGGCTGTGGAGAGCGTGGAAATGAAATGGCTGAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------gtaccttgtgacactctctggttttgttccatt-taattactg---gatagattgaatttccaaag------ctaacttttt---cttatttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG
                                                 |   ||   | | | | | |  ||| |    |  |  |||||   | |     || || |   |       |||| ||| |   ||  | |    |||| ||||||||| |||||||||| |||||||| ||||||||| | || |||||||||||||||
gtgattggcttcaccttattgtgtttggagacatagtaaagcatcgtctttgtttaccataatttattgggttgataagctgcagatactgcgagctgtcacgatttccttgaaatggttctaattttatgtgctgctgtgtgcagTATTCCAACTCTAATGCTGTTGTCTATGTTGGCTGTGGAGAGCGTGGGAATGAAATGGCTGAG

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|116482299|gb|EG524891.1|EG524891
EST:     CTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCAAG                         TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAAT
genomic: CTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCAAGgtaccttgtg ... atttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAAT
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     TGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCCAAG                         TACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAA
genomic: TGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTT-CCAAGgtaccttgtg ... atttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaattactggatagattgaatttccaaagctaactttttcttatttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG
                              agctaac  putative branch site (score: 2)
                                    ctttttcttatttac  CT-rich tract
                                 taactttttcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccttgtgacactctctggttttgttccatttaattactggatagattgaatttccaaagctaactttttcttatttacatagTACTCCAACTCTGATGCTGTTGTGTATGTTGGTTGTGGAGAGAGAGGAAATGAAATGGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA