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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatcattcacgcgcttttcttaaaacgttatcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA

Basic information

species Arabidopsis thaliana
transcript AT5G46110.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 1
gtacgtatcattcacgcgcttttcttaaaacgt-tatc-ctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
||| |  |   |  | |  |  ||     || |  | | |||||   ||||    |||    |||||| || || |   ||  | |   ||   |||| |  |||      ||  || |  ||  |||||||||||||| || || ||||||||||| || |||||||| || || |||||||| ||||| ||
gtatggttttctgccacaataatcgcgtgacctacacctctgcgttgtttattgaattgaattgatttcacagcgattattcagctgtttgaagattgccattttg---tgcaagtgat-cttgtagGTACTTCTTGAACGTTATATTCAACATCCTCAATAAGAAGATATACAACTACTTCCCCTATCCATA

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 2
gtacgtatcattcacgcgcttttcttaaaacgttatcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
                                                      | | | || || | | ||  |  |||| || |   |   ||    | | | |   |||  ||  | | |||||||||| | || || || ||||||||||| |||||||||||||| || |||||||| ||||| ||
-----------------------------------------------------gtacgtttgtttct-ctgcaca--tttgcttcatcacctgttctgtcctgtgtaaacatg-ggcttctgcagGTACTTCCTCAACGTCATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCCTATCCATA

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 2
gtacgtatcattcacgcgcttttcttaaaacgttatcctgcgcactttagcagattcttatgattttaccgccaagttttggtttag------tgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
       ||||   ||       || | ||| |  | |    | ||| | | |  ||  |     | |     || |  || || |       ||    | |  |  |||| ||  |||     ||| |||||| ||| | || || || ||||||||||| |||||||||||||| || |||||||| ||||| ||
--gtaggtcatcaccgttaccaactaacaacatc-tacaattctcttcaacgg--tcagaaagagtcaaaataaaatggtgattcaaaatccctgtttctgggtgtcttta-ccaaattgtactttttcagGTATTTCCTCAACGTTATATTCAACATCCTCAACAAGAAGATCTACAACTACTTCCCATATCCTTA

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S450_22V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------gtacgtatcattcacgcgcttttc----ttaaaacgtt---atcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
                                     | | | | |  |  |  | |       ||| | ||    |  |||||  ||| ||  |||     || |||    | ||       ||||   |   ||| |   | | || ||  ||  |||||   |||||||||||||| || || ||||||||| | |||||||||||||| || || || || || |||||
gtacacattctactcttgtgcagtgctattgagccaaatgcaccgtctattctgtctcaacagctaagatgtctgaaaactgcgt-cttgagatgatctccctgctttctgaggcagtcaggagtttcagggagattaa-aatgtaatgcttgttgtgtatt---agGTACTTCTTGAACGTCATCTTCAACATCATGAACAAGAAGATCTACAACTATTTTCCCTACCCCTA

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S450_17V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacgtatcattcacgcgcttttcttaaaacgttatcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
                 ||  |  || ||     ||| || |           ||||   |  ||||   |     |   | || || || |  ||| ||  | || |   ||  || |   |||||||||| ||||||| || ||||||||| | |||||||||||||| || ||||| || || || ||
-------------ggctgcgctgtttgaatatgcatcatgag-------atgcattcccttctttttgtggttgtctagagtttcagggcta--tgatgccgtgatgcctgttgtgtgt---cagGTACTTCCTGAATGTTATCTTCAACATCATGAACAAGAAGATCTACAACTACTTTCCCTACCCTTA

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtatcattcacgcgcttttcttaaaacgttatcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
                                       ||   ||||  |    |    | ||||| |        |||  | |  ||| |||          ||| || ||      || |||||| ||  | |||||||| |||||||||||||||||||||||||| ||||| || |||||||| ||
-----------------------------------gtaggcatgctttttcttccttcc-ttattttgcttttccacttttctctcttgcaaatgag-------atcttccttc-----ttgcagGTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATA

upper sequence: AT5G46110.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ38162 (Selaginella moellendorffii), 3'ss of exon 1
gtacgtatcattcacgcgcttttcttaaaacgttatcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
                                      |  |||   |      | |||    |||| |        | |  | |  ||| |||          ||| || ||      || |||||| ||  | |||||||| |||||||||||||||||||||||||| ||||| || |||||||| ||
-------------------------------------gtaggcatgctttttcttccttccttttttgcttttccactgttctctcttgcaaatgag-------atcttccttc-----ttgcagGTATTTTCTCAATGTGATCTTCAACATCCTTAACAAGAAGATCTACAATTATTTTCCTTATCCATA

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|124952343|gb|EL027622.1|EL027622
EST:     TCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: TCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
EST: gi|116415580|gb|EG458172.1|EG458172
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
EST: gi|124849971|gb|EH934408.1|EH934408
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GT-CTTCTTGAATGTGATTTTCAACATCCTTAA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAA
EST: gi|116474259|gb|EG516851.1|EG516851
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
EST: gi|124763359|gb|EH853489.1|EH853489
EST:     AGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAACGTGATTTTCAACATCCTTAACAAGAAGATCTA
genomic: AGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTA
EST: gi|116474248|gb|EG516840.1|EG516840
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
EST: gi|116431239|gb|EG473831.1|EG473831
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
EST: gi|124869960|gb|EH954397.1|EH954397
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATC
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATC
EST: gi|164062801|gb|ES213614.1|ES213614
EST:     CTTCTTCATGTG                         GTACTTCTTAAATGTGA-TTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: CTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
EST: gi|125306329|gb|EL320414.1|EL320414
EST:     TCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAAGAAGATCTATAATT
genomic: TCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAAC-AAGAAGATCTATAATT
EST: gi|116420927|gb|EG463519.1|EG463519
EST:     TTTCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
EST: gi|116431241|gb|EG473833.1|EG473833
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCATTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGAGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
EST: gi|124926331|gb|EL004187.1|EL004187
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGCGATTTTCA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCA
EST: gi|124948913|gb|EL024608.1|EL024608
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGA
EST: gi|116474253|gb|EG516845.1|EG516845
EST:     TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTG                         GTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA
genomic: TTCCTCGCCAAGTATCCATGGCTAGTCACTGGATTCTTCTTCTTCATGTGgtacgtatca ... gtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA
                     aattgac  putative branch site (score: 3)
                                              tatttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtatcattcacgcgcttttcttaaaacgttatcctgcgcactttagcagattcttatgattttaccgccaagttttggtttagtgcgaattgacgcttttatcctcatttggtatttacagGTACTTCTTGAATGTGATTTTCAACATCCTTAACAAGAAGATCTATAATTACTTCCCTTATCCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG