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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG

Basic information

species Arabidopsis thaliana
transcript AT5G11950.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g51210.2 (Oryza sativa), 3'ss of exon 3
--------------gtgagaaaacgctttaaaactgaatc--ctagctaattgttaaagttgaaa-gttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
                 | |       || | |||   |   |  ||||||  || ||      | | ||   ||   | ||||     ||       |||||| |||||||||||||||||| |||| ||||||||||| |||||||||||||| || ||| | ||  | 
gtattacactcagttctacatgttttcttgatactatttgaacgggctaatatttcaaaccaccatgcttaattactgacaacttttttgtggacaatagGAGGGTATGGAACAATGGAGGAGTTGTTAGAGATGATAACTTGGTCACAACTTGGAATTCATGACAAACCA

upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g46360.2 (Oryza sativa), 3'ss of exon 4
------------------------------------------------gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
                                                 | || |    ||||  |||   ||| || |  | |  |||  |||| | ||    | | |     |    | ||||  ||||| || ||||||||||||||||||||||| ||||||||||||||||  |||||||| || ||| | ||| | 
gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatc-tatcacactagtaa--ttgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCA

upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g46360.3 (Oryza sativa), 3'ss of exon 4
------------------------------------------------gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG-----------------------------
                                                 | || |    ||||  |||   ||| || |  | |  |||  |||| | ||    | | |     |    | ||||  ||||| || ||||||||||||||||||||||| ||||||||||||||||  |||||||| || ||| | ||| |                              
gtaattgataattccaatatatgtgagatggactgacgatctgaaatgttcagtaccttctttctaacatcatc-tatcacactagtaa--ttgataattcaaatgtaacttggttattgatttttatcagGGGGCTATGGAACAATGGAGGAGCTGTTAGAGATGATAACATGGTGCCAACTTGGAATTCATGACAAGCCAGTAAGCATAATTGAGATATTTGATACTAG

upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G008726_T01 (Zea mays), 3'ss of exon 4
------gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttg---ttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
           | | |   ||       | | |  |||    |  | |  |      |||| |||     |  |||||  | ||    |||||||| || ||||||||||| || ||||| ||||||||||| |||||||| || || || ||| | ||  | 
gtacacaatctacatcttctttttctccagtacatgctggcagcgacatgtatctcgtttgatat-ggcgatgacgggtctctggacatcagGAGGGTACGGAACAATGGAAGAACTGTTAGAGATGATAACGTGGTCACAGCTCGGAATTCATGACAAACCA

upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G05560.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------------gtgagaaaacgctttaaaactgaatcctagctaattgt-taaagttgaaagttttggtatcaaaaac-tacggggttttgt--tcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
                                                                                                              |    |    | |||  |      |  ||  | ||| | ||   |    | | |   | ||   |   | |      || |  | |||||| |||||||| |||||||||||||||||||||||||| ||| | |||||||| |||||||| ||  ||
gtacttttacatcaacagctctcaaataattttaagaaataattgatgattacatgtttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttggattcatggtgttttggattgttgttgta-ttgattatgtactatatggactctcactgtcgttattatgcctccccttataattagGAGGATATGGAACCATGGAGGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG

upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------------gtgagaaaacgctttaaaact----gaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttt----------------tgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
                                                                                            ||  | |||    ||   | |    |  |  | | |  |||||  | |    |  |    |||  |     || |   ||                |  | |||||| |||||||| ||||| |||||||||||||||||||| ||| | |||||||| |||||||| ||  ||
gtagtaacctcaacatctctcaaataattttaaaaaataattgttgattacatgtcttatacatgtgaatgccactaaaattgttcttaattgtacggaaatttgtttgtattcttggtgttttggattgttgttgtattgattatgtactatatggactctcactgtccttattatgcccccccttataattagGAGGATATGGAACCATGGAAGAGCTGTTGGAGATGATAACTTGGGCCCAACTTGGAATCCATAAAAAACCG

upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G11070.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------------------gtgagaaaacgctttaaaac-tgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
                                                                                                                    ||     |  ||| ||   | || ||  |||| ||||  ||    |     || |  || |       |     || |  | |||||| |||||||| ||||| |||||||||||||||||||| ||| | |||||||| || ||||| ||   |
gtagttaccacaagagctttcaaatagttttaaaaataattgatgattgtttgtcttatgacatgttaatgttgctaaagatgttctttttatatactgaaatttactattttgatgtactggattgctgtattgcatgtataatagc-aattactatttct-----ttcttataccctctctcatttccttataattagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACAG

upper sequence: AT5G11950.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------------------------------------gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgtt----cagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
                                                                                                             |    |    ||| |   ||| ||  |   ||  |  ||    | |   |||   | | | |  ||      |||  ||     |||||| |||||||| ||||| |||||||||||||||||||| ||| | |||||||| || ||||| ||  ||
gtagttaccacaacagctttcaaatagtttcaaagaataattgatgactgtgtgtcttatgacatgttaatgttactaaagatgctctttcatatactgaaatttactattttgatgtacttgattgctgtattgtgtata--taatagtagttactatttctttcttataccctctctcatttccttataatagGAGGATATGGAACTATGGAAGAGCTGTTGGAGATGATAACTTGGGCTCAACTTGGAATTCATAAAAAACCG

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|125279367|gb|EL293452.1|EL293452
EST:     GCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG                         GAGGTTATGGAACAATGG
genomic: GCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTGgtgagaaaac ... ttttgttcagGAGGTTATGGAACAATGG
EST: gi|19874754|gb|AU235585.1|AU235585
EST:     GCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG                         GAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAAC
genomic: GCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTGgtgagaaaac ... ttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAAC
EST: gi|19740964|gb|AU226317.1|AU226317
EST:     GCGAAAGGCTGCAATGGCACA-GAAGCTGAGGCCTTCATTGCACTCCCTG                         GAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAAC
genomic: GCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTGgtgagaaaac ... ttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAAC
EST: gi|124719038|gb|EH810440.1|EH810440
EST:     CGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG                         GAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGT
genomic: CGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTGgtgagaaaac ... ttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG
 agctaat  putative branch site (score: 3)
                                             ttttgttc  putative PPT
     attgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaaaacgctttaaaactgaatcctagctaattgttaaagttgaaagttttggtatcaaaaactacggggttttgttcagGAGGTTATGGAACAATGGAGGAGCTGTTGGAGATGATAACATGGTCACAACTTGGTATCCATAAGAAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG