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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttaagtgtttgtgagatttgtacctaagatgaagttagttctctttgtggtttctcttcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG

Basic information

species Arabidopsis thaliana
transcript AT1G14510.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g14010.2 (Oryza sativa), 3'ss of exon 1
ctttttaagtgtttgtgagatttg--tacctaagatgaagttagttctctttgtggtttctc------ttcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG
       | ||||| |  | |  |  |   |  ||| |  | | |||  |       ||  |         ||||  |  |  |||||||  || ||| | | ||||||||| || || |||||| | ||||| ||||| |||||||||||||| || ||  | || | ||||||||| ||||| |||||||| ||||||||  | ||
-----ccaatgtttcttggctacgatttatttcgattatataacttccatgaaaaaatttccagaaaacgattgatatgcttctgaatta--ttgtttac-attgcagAGAAAGAGAATTTGTGTTTATATGGTCTTCCCAATGAGACATGGGAAGTGAACTTGCCTGCTGAGGAGGTTCCTCCAGAGCTTCCAGAACCAGCTCTGGG

upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G107807_T01 (Zea mays), 3'ss of exon 2
ctttttaagtgtttgtgagat-ttgtacctaa-gatgaagttagttctctttgtggtttctct-tcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG
     | |   |  || | || |  || |||  || |     |  ||   ||    || || | | ||| | | ||     ||| | ||  ||  ||   ||||||| || |||||||| ||||||||  | ||||||||||| |||||||||| |||||| | |||||| || |||||||||||||| ||||||||  | ||
---actgatgttcagtaacatgtcataactagtgacgtgaacatatcagattccatttcctttgttttgtcctgttgacatatttctttcctttttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTTACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG

upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G063864_T01 (Zea mays), 3'ss of exon 2
ctttttaagtgtttgtgagatttgtacctaagatgaagttagttctctttgtggtttctcttcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG
  |  |      |  |  |   | |   | | |||||   |      |   |  ||| |  | ||| |   ||     | | | || |||  ||   ||||||| || |||||||| ||||||||  | ||||||||||| |||||||| | |||||| | |||||| || |||||||||||||| ||||||||  | ||
actgatgttcagtaatatgccatattgttgacatgaacacatcagattccatatttttttgttttgtcccgttgacatagtgctttctttcttatgccagAGAAAGAGAACTTGTGCCTTTATGGTTTGCCAAATGAGACTTGGGAGGTCACTCTTCCAGCTGAGGAAGTACCTCCTGAGCTTCCAGAACCAGCACTGGG

upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G153087_T01 (Zea mays), 3'ss of exon 2
-ctttttaagtgtttgtgagatttgtacctaagatgaagttagttctctttgtggtttctcttcttgacttcttagtga-attacgtttttt--gctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG
 |||  |   | |||||  ||  || | |||   |    ||||     | ||      ||     |  ||| || | || ||||  || |||    |    |||||||||| ||||| ||| | ||||||||||| ||||||||||||||  | ||  | || | ||| |||||||||||||| || || || |||||  | ||
tcttgattcatttttgtttgaagtg-agctattttaggtttagag---tctgaaacaactgcaaataccttattcgagatattattttcttttgttttgcacagAGAAGGAGAACTTATGTTTATATGGACTTCCTAATGAGACATGGGAAATAAACTTGCCTGCTGAAGAGGTCCCTCCTGAACTGCCAGAGCCAGCTCTTGG

upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G115424_T02 (Zea mays), 3'ss of exon 1
ctttttaagtgtttgtgagatttgtac-ctaagatgaagttagttctctttgtggtttctcttcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG
 | ||      |||   |     | |  | |   |  | ||||  |            |   |      |||  | |    |    ||||   |   ||||||||||| || || ||| | ||||||||||| |||||||||||||| || ||  | || | ||||||||| |||||||| || || || |||||  | ||
-tcttggttcattttcaattaaagcaagccattttagatttagagcctgaaacaaccgcaaataccttattcgaaatattattttcttttgttttgcgcagAGAAGGATAATTTATGTTTATATGGACTTCCCAATGAGACATGGGAAGTAAACTTGCCTGCTGAGGAGGTTCCTCCTGAACTCCCAGAGCCAGCTCTCGG

upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0035g01980.t01 (Vitis vinifera), 3'ss of exon 2
ctttttaagtgtttgtgagatttgtacctaagatgaagttagttctctttgtggtttctcttcttgacttcttagtgaattacgttt-----tttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG
     | | | | | |    ||| ||| | |     |  ||  |    |||   |   |       ||||  |  |     | ||||     |||| |  |  ||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| || || ||||||||||| |||||||||||||| |||||||| |||||
-----ttattttatattcactttttacattatccatatatatcttatgttggcataaatgagtgcaacttgcttattttggatgtttgtaaatttgttcttatagAGAAGGAGAACTTGTGTCTGTATGGACTTCCAAATGAGACATGGGAAGTTAACCTGCCTGTTGAGGAGGTACCTCCTGAGCTTCCAGAACCAGCATTAGG

upper sequence: AT1G14510.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ23237 (Selaginella moellendorffii), 3'ss of exon 2
-----------------ctttttaagtgtttgtgagatttgtaccta---agatga-agttagttctctttgtggtttctcttcttgacttcttagt---gaattacgttttttgctaatg----cagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG
                    ||||      ||||    |  ||| |    | || |  ||  | ||| ||  |    | |  | |||||||    ||   |  | || |||| |  || ||    ||||||||||||| ||||| |||||||| || ||  | ||||| |||||||| |||||||| |  ||||| || || || ||||| ||||| |||||| | ||
gtttgtactctttcttatcctttagtctagtgtggtgctactacatgtatatataatggtcgggtcttttgtttaagtgtgatattgactttggtgtatggtgtcactttttctcttattgactccagAGAAGGAAAATTTGTGCCTTTATGGTCTCCCCGACGAGACTTGGGAGGTGAATCTTCCAGCCGAGGAAGTGCCGCCGGAGCTCCCTGAGCCAGCGCTCGG

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|86050925|gb|DR346680.1|DR346680
EST:     ATGTACAGAAGTTTTACCATCAGTGTGACCCTG                         AGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
genomic: ATGTACAGAAGTTTTACCATCAGTGTGACCCTGgtgagttatt ... gctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
EST: gi|86050929|gb|DR346684.1|DR346684
EST:     ATGTACAGAAGTTTTACCATCAGTGTGACCCTG                         AGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
genomic: ATGTACAGAAGTTTTACCATCAGTGTGACCCTGgtgagttatt ... gctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
EST: gi|86050926|gb|DR346681.1|DR346681
EST:     ATGTACAGAAGTTTTACCATCAGTGTGACCCTG                         AGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
genomic: ATGTACAGAAGTTTTACCATCAGTGTGACCCTGgtgagttatt ... gctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
EST: gi|86050928|gb|DR346683.1|DR346683
EST:     ATGTACAGAAGTTTTACCATCAGTGTGACCCTG                         AGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
genomic: ATGTACAGAAGTTTTACCATCAGTGTGACCCTGgtgagttatt ... gctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
EST: gi|125201374|gb|EL216328.1|EL216328
EST:     ATGTACAGAAGTTTTACCATCAGTGTGACCCTG                         AGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACA
genomic: ATGTACAGAAGTTTTACCATCAGTGTGACCCTGgtgagttatt ... gctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACA
EST: gi|86050924|gb|DR346679.1|DR346679
EST:     ATGTACAGAAGTTTTACCATCAGTGTGACCCTG                         AGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
genomic: ATGTACAGAAGTTTTACCATCAGTGTGACCCTGgtgagttatt ... gctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
EST: gi|86050933|gb|DR346688.1|DR346688
EST:     ATGTACAGAAGTTTTACCATCAGTGTGACCCTG                         AGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA
genomic: ATGTACAGAAGTTTTACCATCAGTGTGACCCTGgtgagttatt ... gctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgtggtttctcttcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG
                                            tgctaat  putative branch site (score: 2)
                                       ttttttgct  CT-rich tract
                                       tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttaagtgtttgtgagatttgtacctaagatgaagttagttctctttgtggtttctcttcttgacttcttagtgaattacgttttttgctaatgcagAGAAGGAAAACTTGTGTCTTTATGGACTTCCAAATGAGACATGGGAGGTTAATCTTCCCGTTGAGGAGGTCCCTCCTGAGCTTCCTGAACCAGCGTTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - -tgtttgt
- - - - - - - - - gatttgt
- - - - - - - - - - - - - - -aagatga