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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccttatgtcactaatacatatcatactccacttcctgagtcttactgtttttggctgattattcgttcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G56280.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g39070.1 (Oryza sativa), 3'ss of exon 5
---------------gtgagccttatgtcactaatacatatcatactccacttcctgagtcttactgtttttggctgatt---attcgttcatat------gcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG
                | | |  | | |  || | | ||||     |  ||| ||  |    || |||||||||   | |   | |     ||||      ||||||||||||||||| || || ||||| ||||||||||||||||| ||||||||  || | ||  |  | ||| |||||| | | ||||||||||
gtgagggttcttcttatcatcagtttatgtcttacagatattgagttgtactacccaa--tatattgtttttggaaaaatgatactgacagatatatttgagcagTGGCTGCTCATCTGACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAATATCTTGTTTCCATGCAGAAAG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G028089_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------gtgagccttatgtcactaatacata-tcatactccacttcctgagtcttactgtttttggctg-attattc---gttcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG
                                                               ||| || ||   |    || | ||| ||||| |  |      |  | || |||  |     || | ||  |   | |  | ||||||||||||||||||||| || ||||| ||||||||||||||||| ||||||||  || | ||  |  | ||  |||||| ||| ||||| ||||
gtaagcattctactttgaagccctctctcaaaacaaatttatgggtcagtgggtgtcttccccgtg-gctttgctttctcaacaaatagtcatatt--atccgaggtatttttctggatagaaatgtactaaacgatgcttttgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTTGTTGCCATGCAAAAAG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G080652_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------gtgagcct--tatgtcactaatacatatcatactccacttcctgagtctt---actgtttttggctgattattcgttcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG
                                                       |||    |  | | |||  | ||    |||||||        |   | |    || |  ||   || ||   |  ||    ||||||||||||||||||||| || ||||| ||||||||||||||||| ||||||||  || | ||  |  | ||  |||| | ||| ||||| ||||
gtaagagttataatttgaagacatctcataagacagccctgggggtgtcttccctgtggctttgctttctcaacattattagtcatactgtctgaggtatatttctggacagaattgtactaatcgatgattt-cgtgcagTGGCTGCTCATCTTACAGGAATACACAGTGCCATCAAGATGCTCAATAGCAGGGTCCGTGTTATCCATCAGTATCTCGTTGCCATGCAAAAAG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 5
-------------gtgagccttatgtcactaatacatatcatac-tccacttcctgagtcttactgtttttggctgattattcgttcat-----atgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG
              ||    | |   |||  |      | |    |    ||  | |||  || ||  | |  || ||  | | |   |     |||||||||||||||| |||||||| ||||| ||||||||||| |||||| |||||||||| |  |||||  | ||  |||||  ||||||||| ||||
tgttgattgatgcatgtaagtgactccacctagtggggtaaggtgtgggtttttttagttgtattgcatgtatctaatattccatgttttcttaatgcagTGGCTGCTCACCTTACTGGAATACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACATCACTATCTTCTTGCAATGCAAAAAG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 5
--------------gtgagccttatgtcactaatacatatcatactccacttcctgagtcttactgtttttggctgattattcgt----tcatat-gcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG
               ||    | |   |||  |     || |      | ||  | ||| ||| | | | |  || ||  | | |    || |||  ||||||||||||| |||||||||| ||| ||||||||||| |||||| |||||||||| |  |||||  ||||  |||||  ||||||||| ||||
aatgttgttgattgatgtaagtcactgcacctagtgggattagttgtgatttttttagttttattttatgtatctaatattccatgttttcttattacagTGGCTGCTCACCTTACTGGTACACACAGTGCCATCAAAATGCTTCATAGCAGAATAAAGGTGCTACACCACTATCTTCTTGCAATGCAAAAAG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------------------------gtgagccttatgtcact-aatacatatcatactccacttcctgag-----tcttac---tgtttttggctgattattcgttcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG
                                                                            |      ||||     | ||||||||| || |     ||   ||      ||||     ||  |||       |     |   | |||||||||||| || || || || ||||||||||||||||||||||| |||||||||||| | || ||| | ||  ||||   ||| ||||| ||||
gtaagcccttatctccaccatcatttcttgtcttgtctcttaccatttttgcagaaaattataaactagttctacagaagtttttatccttttcaatacatattatgcatttttttaagaaaaaaatcttgtgaatggctttacaactgtggctatgtttgtgcagTGGCTGCCCACCTCACGGGGATACATAGTGCCATCAAGATGCTAAATAGCAGAATCCGTGTTCTTCATCATTATCTGCTTGCTATGCAAAAAG

upper sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S34_439V6.1 (Physcomitrella patens), 3'ss of exon 5
------------gtgagccttatgtcactaatacatatcatactccactt-----cctgagtcttactgtt----tttggctgattattcgttcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG
            |   |  | |||||| |   |  | |||   || |        | ||  | | || |||    ||| |  | |  |  | |    |||||| ||||||||| | || || || ||||||||||| ||||||||||||||||| ||  ||||  | || ||  | |||||| | || |||||||
tggatgtattttgaaggaatgatgtcattg-catctgtcactgtctaacaaatggcgtggttttcacagttaaaattttgtgggtcttgtggttgc-tgcagTTGCTGCTCATTTGACCGGGATGCATAGTGCCATAAAGATGCTTAATAGCAGGATTCGAGTTTTATATCACCACCTTGCTTCTATTCAGAAAG

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|125084826|gb|EL144899.1|EL144899
EST:     TCATGTTGCACATC-TAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT                         TGGCTGCTCATCTTACTGGTATACATAGTG
genomic: TCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGTgtgagcctta ... tcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTG
EST: gi|19876192|gb|AU237023.1|AU237023
EST:     TCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT                         TGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCG
genomic: TCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGTgtgagcctta ... tcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCA
EST: gi|86085218|gb|DR380977.1|DR380977
EST:     TCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT                         TGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCA
genomic: TCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGTgtgagcctta ... tcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCA
EST: gi|86054006|gb|DR349763.1|DR349763
EST:     TCANNNTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGT                         TGGCTGCTCATCTTACTGG
genomic: TCATGTTGCACATCTTAAACCATCTGACGGAGGCTCAGCAGCAACCCAGTgtgagcctta ... tcatatgcagTGGCTGCTCATCTTACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catactccacttcctgagtcttactgtttttggctgattattcgttcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG
                                        ttcgttc  CT-rich tract
                                  tgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccttatgtcactaatacatatcatactccacttcctgagtcttactgtttttggctgattattcgttcatatgcagTGGCTGCTCATCTTACTGGTATACATAGTGCCATCAAGATGCTTAATAGCAGAATCAGAGTGCTTTACCAAAATCTTGCTGCAATGCAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC