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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT

Basic information

species Arabidopsis thaliana
transcript AT3G13580.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g51630.2 (Oryza sativa), 3'ss of exon 6
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                                                       || |  ||    | || | ||| || |  |       || ||||   |   ||  |  | |  ||| |   ||| |||||||  | || ||||||| |||||||||| ||||||||||  | |||||||||||||| ||||| |||||||||||||| ||||| |||||  | |||||||
-----------------------------------------------------------------------------------------------------------------------gtttgcca--ccttgaatctcacttgttctgcttttactgtgtcaattg-gtacct-tacagtcttggtgtttgtatcagGGTTTGGGTAAGCATGACATCATCTGCATTGAGGATCTTGTTCATGAGATCATGACTGTTGGCCCACATTTCAAGGAGGCCAACAACTTCCTCTGGCCAT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 6
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                           ||||  |      ||| || ||  ||| || |   | |||||      ||||||     ||   || |  |||| | |       | |||  || |      | | ||||  | || ||||||| |||||||||| ||||||||||  |||| ||||||||||| || || ||||| |||||||| ||||| |||||  ||||||| |
-------------------------------------------------------------------------------------------gtatgtttgctcttgtaggctttcatt-gtgttgtatatatg-----ccatttacagctaa---tcaaattcttatttg-----gcctattgttggtcaacca-ttagGGCTTGGGGAAGCATGACATCATCTGCATTGAGGATCTTGTCCACGAGATCATGACTGTCGGTCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCCT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G094051_T05 (Zea mays), 3'ss of exon 5
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                                 |  | ||  | | | || |    |||      | ||   |||   ||||     | | | ||  |  |    || |  ||    | |||| ||||  |||||||  | || |||||   |||||||||| ||||||||||  | || ||||||||||| ||||| ||||| |||||||| ||||| |||||  |||||||||
-----------------------------------------------------------------------------------------------gtttgtaaacttggaactctac--atctggttcctgtgttctgt---ttatatatgacaatttacatgatg---atctccac----cttttggtgttctatcagGGCTTGGGCAAGCACAACATCATCTGCATTGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCCAACAACTTCCTGTGGCCAT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G344279_T01 (Zea mays), 3'ss of exon 6
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                                 |    ||  |||||     |   |||      | ||   |||   |  |  |  | | |  |    ||   |     |    | | |||| ||||  |||||||  | |  |||||    ||||||||||| ||||||||  | || ||||||||||| ||||| ||||| |||||||| || || |||||  |||||||||
------------------------------------------------------------------------------------------------gtttgtaaacttggaactg-tacatctggttcctgtgttctgtttatatttgtttatatttgacaatttacatgatgatctccaccttttgttgttctatcagGGCTTGGACAAGCAAAAAATCATCTGCGTCGAGGATCTTGTTCACGAGATCATGACTGTTGGCCCACACTTCAAGGAGGCGAACAACTTCCTGTGGCCAT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G100225_T01 (Zea mays), 3'ss of exon 5
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                     |   |  |||  || || |   ||  |     | ||     || | ||| |    |||  | |   ||      |   || ||||      |||||   | || ||       || |||    |  | |||| || || |||||    ||||||||| ||||||| ||  |||| |||||||||||||| || || || |||||||| ||||| |||||  | ||||| |
--------------------------------------------------------------------gtttgtcacctgcaacaactaccgtgctgattccgata----atccgattaggtccaca--tttcagttccagccttagataaaaaa---gagtctttgttttactt------tctgtgc----gtgttagGGCCTCGGGAAGCACAATATCATCTGCATTGAGGACCTTGTCCACGAGATCATGACGGTCGGCCCGCACTTCAAGGAGGCCAACAACTTCCTCTGGCCGT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G18170.1 (Glycine max), 3'ss of exon 6
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                          |   |  |  || ||  || | ||  | |||   | | |  |  ||||    ||      |  |||   | | ||  |     | ||||| | ||   ||    |        | || |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| || || |||||||| ||||| || ||| ||||||| |
-----------------------------------------------------------------------------------------gtccgt-gtggtctattctgtagtcc-tctgt---aaacacttccattgcttgtttgttctattacttagtttttttccc----tgacataacattcaatgccagACT-----TTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATCATGACTGTTGGACCTCACTTCAAGGAGGCCAACAATTTTCTGTGGCCTT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 6
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                               | |      |||       | |     | | | || |  ||||    ||      |  ||||  | | ||| ||      ||||| | ||   ||    |        | || |||||||| ||||| |||||||| |||||||||||||||||  |||| ||||| || ||||||||||| ||||| || ||| ||||||| |
----------------------------------------------------------------------------------------------gtctgtctggtgtaccggctagtcatctttaaatatctccattgcttgtttgttctattactcagttttttcgctg-----acataacattcaatgccagACT-----TTGGGGAAGCATGGGATCATTTGCGTTGAAGATCTGATCCATGAGATATTGACTGTTGGACCTCATTTCAAGGAGGCCAACAATTTTCTGTGGCCTT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 6
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                                         ||| | |  |  ||   |||||  |||   ||   || |||    | ||     || ||| || ||      | ||  |    ||||    ||||   | || |||  ||| ||||| ||| |||| ||||| ||||||||||| ||||| ||||||||||| |||||||| || || |||||  |||||||||
---------------------------------------------------------------------------------------------------------gtttgttgtaggttaaataacatttatatgtt-cgatgtattgctataaac---tggcttttcaatg-----acattttggtatgttattgcagGCTTTGGGCAAGTTTGGAATCATTTGCATTGAAGATCTCATCCATGAGATTATGACTGTTGGGCCACACTTCAAGGAGGCAAACAACTTCCTGTGGCCAT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 4
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttg-gattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                           |||| |  | |    ||| ||  |||||     ||    || |   || | | |||| |    |     ||  ||| |   ||  |    ||  ||| | |||  | |||  || ||||||   || ||||| ||  |||||||||| || ||||||||| | || ||||| || || |||||||||||||| |||||||| ||| | |
-----------------------------------------------------------------------------------------tcgtataaatagctgcattgcgacacaattaa---aattagtaggacctgacgtgtatcctttgca----gtgatttcacctgatgaat---tctgttgattttgtgt-agGCACTTGGAAAGTTGGGTATCATATGTATTGAGGATCTCATTCATGAGATCTTCACTGTTGGACCTCACTTCAAGGAAGCCAACAACTTTTTATGGTCTT

upper sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 5
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaact-ctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                                                                                                                                    | |   || |||   |  |  ||| |||  |||  ||  |  |||  | | ||||         |||| | || || ||| |||| ||||||||  | |||||||| ||||| ||||||   |||||||||||||| |||||||| || |||||||| |||||||| |
------------------------------------------------------------------------------------------------------------------------------------gtacgatccttttctacgatgacttctagttctcatcgtttcttatttgttctttc--------tcagAGCCTGGGGAAGTATGGAATCATCTGTATCGAGGATCTCATCCACGAGATCTACACGGTTGGGCCACACTTCAAGGAGGCGAATAACTTCTTGTGGCCTT

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|86083877|gb|DR379636.1|DR379636
EST:     AGCTTAACCACCAGAGGATTGCCTTAACAGACAATTCTATTGTAGATCAG                         GGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATC
genomic: AGCTTAACCACCAGAGGACTGCCTTAACAGACAATTCTATTGTAGATCAGgtgcatatca ... gttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATC
EST: gi|164219486|gb|ES147354.1|ES147354
EST:     AGCTTAACCACCAGAGGACTGCCTTAACAGACAATTCTATTGTAGATCAG                         GGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATC
genomic: AGCTTAACCACCAGAGGACTGCCTTAACAGACAATTCTATTGTAGATCAGgtgcatatca ... gttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT
                      tctatatttacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcatatcatcaacctatctccttcatcaagtctggttcagttcctaaagtcaatattattgccgttatccctgtcctagaaaaaatgatgtattatcatcaatgttggattcaatttgtctaacagatatggattgtcatttatcatcaaaactctatgtcttctctatatttacatatcctttgctgttgaatcagGGGCTAGGAAAGCATGGCATCATCTGCGTTGAGGATCTGATCCATGAGATCATGACGGTTGGGCCACATTTCAAGGAAGCCAATAACTTTTTGTGGCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA