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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA

Basic information

species Arabidopsis thaliana
transcript AT5G61840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                                       |  | |    | ||||  || |||    | |     | || ||  |  ||   ||   || |  |   |  | | ||  ||||||   |  ||| |  ||      ||| |||||  | ||| | || ||||| ||||||||  ||||||| || ||||||||||| ||||| |||||| |||| || || |||||||||||| |  | 
--------------------------------------------------------------------------------------gtgagcaccaagaacatgcaa-tcactcgatgcttcctcataagcattgttgatgaattattg--taacccaaaagtct-tgatgaacctgctttatgcaat----gcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 3
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                       |||||  | |||| || |  ||     |  ||  || |   |    |   |||| |    ||     |    ||  ||  | ||||  | || | |||||   || |  |||         |||| |||||  | ||| | || ||||| ||||||||  |||| ||||||||||||||||| || || |||||| ||||||| || || ||||||||| |  | 
----------------------------------------------------------------------gtaattcatctatctgtctacaa-----gcaatgcaattggcacctcgctcatttttggtcctcccactgcttcctgggtctattctc-tgatgactgatggcatt-gcctgttc------tacagAGGTGCTCGTGCATCGGTCTGGGAGAACTTCAAGAACAACCCGCTGTTTGACATCTCGACCGATCACCCACCAACATACTACGAAGACATGCAGCGCTCG

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G448834_T02 (Zea mays), 3'ss of exon 2
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                                         | || |   | |        |     |    |    ||   | ||    || ||     | || ||  ||||         | || | | |  |||  |     |||||| ||  | ||  | || ||||| |||||||| ||||| |||||||| |||||||| || ||||||||  | || || || |||||||||||| | || 
-----------------------------------------------------------------------------------------gcaagtcaagtcg---gctccggtccattccatccaatgccaatgccaatatagtacatgtttatttatatatatgccatggttggtggatgatcatgc--atgcagGGGCGCTCGCGCGTCGGTGTGGGAGAACTTCAAGGACAACCCGCTGTTCGACATCTCGACGGAGCACCCGTCGACGTACTACGAGGACATGCAGCGCGCC

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                                     |  || | ||| ||    |   ||  |       |    || || |  |  |    | | ||  ||  | || | |        |||  | |  || |  | ||   |||| ||||| |||||||| || ||||| ||||| || |||||||| ||||||||||| || |||||||| ||||||||||| || |||||||||||  |||| 
------------------------------------------------------------------------------------tgcatgaagttt-ggttccatgtcttgatgctttca----taccaaaacgaat----aacaataaatgatcctgaaagctcaaactgac-tgtacttttgtatct--tacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 3
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                               | | |      ||| |||||    |   ||  | | |  ||||   || |               ||   | || || |  || |  | |   ||  |||   |     |   | || ||||| |||||||| || ||||| ||||| || |||||||| ||||||||||| || || ||||| |||||||||||||| ||||| |||||  |||||
-------------------------------------------------------------------------------taagcatgcatgaagtttggttccatgtcttgatataccaaaacaaatga---------------caaaaaatgatcctgaaagc--tcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                                        || | ||| |  |||  ||        | |      || || |      || || | |   ||  | ||     |   |||   ||   || | |   | |    ||| || ||||||||||| || ||||| ||||| || ||||||| ||||||||||||||| || ||||| ||||| || || || ||||||||||| ||||| 
---------------------------------------------------------------------------------------atgaagtttggtgcatgcaat------gatgctttcataacaaaacacacttggatcaacaaataatcct---ggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                         |||| ||| |  |||    | ||||  ||   | ||  || | | ||  | |  ||   |||||||  | |||    || || || |      ||   || ||||               ||| || ||| | |||||||| ||||| || || ||||||||||| || |||||||||||||||||||||||||  || |||||||||||||||||  | || 
-------------------------------------------------------------------------attgtttttt--gttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttt------tggacatttttg---------------cagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactc---aaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                                                 |||   || |      |  | |      ||| ||    | | ||  |  |  ||| |||     || | |    ||     |  |||     | ||  |||| |||||||| ||||| || ||||| ||||| || ||||| ||||| ||||||||||| || ||||||||||| ||||||||||| ||||||||  | || 
------------------------------------------------------------------------------------------------aggaagcaacatcttgtatgatacatggctttgtctt-ttatattaggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattg--acagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S7_455V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                                     |  || ||  | |    |   | |||      |   ||||||     || ||       | ||| ||||   || |   | ||| | | ||  || |   |       ||| || |||||||||||| | |||||||| |||||||| || ||  |||| |||||||| |||||||| ||| |||| || ||||| ||||||||  | |||
-------------------------------------------------------------------------------------gcatgcaagctagttttt---attcatcttttgtgtatttattcttttgcttcc----tcttggtttgt---tagacatactga-gttcttcattggatgattctttgcagAGGCGCAAGAGCAGCTATCTGGGAAAATTTCAAAGATAACCCATTGTTCGACATCTCGACAGAGCATCCAGCAACTTACTATGAAGACATGCAACGCGCA

upper sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ05285 (Selaginella moellendorffii), 3'ss of exon 3
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttc---ttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
                                                                                                                     | ||| || ||  | |   |  | |  | | | |||      |  || || ||  |||  |||  |  |||        |||||||||  | || ||||| ||||| || ||||| || ||||| || ||||||||||| || |||||||| |  || || ||||||||||||||| |||| 
---------------------------------------------------------------------------------------------------------------------gtaaagttctctcaatacatagaaaagctttgtttgaaaagatcttattccgttctgacattttctgctca------tgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTATGAGGACATGCAGCGAGCT

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|86040267|gb|DR336022.1|DR336022
EST:     GGATTGTTTTATGATGTGGGAAATGACCCTGAGGGTGGGTATTATGCGAG                         GGGTGCAAGAGCAGCTGTATGGGAAAAACTTCAAAGACAATCCGCTGGTTG
genomic: GGATTGTTTTATGATGTGGGAAATGACCCTGAGGGTGGTTATTATGCGAGgtaatttttt ... actggcacagGGGTGCAAGAGCAGCTGTATGGGAAAA-CTTCAAAGACAATCCGCTGTTTG
EST: gi|86040269|gb|DR336024.1|DR336024
EST:     GATTGTTTTATGATGTGGGAAATGACCCCTGAGGGTGGTTATTATGCGAG                         GGGTGCAAGAGCAGCTGTATGGGAAAACTTCAA-GACAATCCGCTGTTTGA
genomic: GATTGTTTTATGATGTGGGAAATGACCC-TGAGGGTGGTTATTATGCGAGgtaatttttt ... actggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
        attgttcttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA