RetrogeneDB ID: retro_tsyr_858

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_220113:2324..3442(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ACTA2
• Ensembl ID: ENSTSYG00000008155
• Aliases: None
• Description: actin, alpha 2, smooth muscle, aorta [Source:HGNC Symbol;Acc:130]

Sequence

>retro_tsyr_858
GAAGATGAAGCCACCACGCTCATGTGTGACCATGACTCTGGCCTGTGCAAGGCAGGCTTTGCAGGATATGATGCCCTGCG
GGCTGTCTTCCCTTCCATCGTGGGCCACCCTCGCCACCAGGGTGTGATGGTGGGAAGGGGCCAGAAGGACAGCTACGTGG
GGGATGAGGCTCAGAGCAAGCGAGGAATCCTAACTCTCAAATACCCGATCGAGCACGGCATCATCATCAACTGGGATGAC
ATGGAGAAGATCTGGCACCATTCCTTCTACAATGAGCTGCATGTCGCACCTGAAGAGCACCCCACCCTGCTCACAGAGGC
CCCCTAAATCCCAAAGCCAACAGGGAGAAGATGACCCAGATCATGTTTGAAACCTTCAACGTCCCTGCCATGTATGTCGC
CATTCAGGCTATGTTCTCCCTCTATGCCTCTGGGCGCACTGCAGGCGTCGTCCTGGATTCAGGGAATGGTGTCACCCCCA
ATGTCCCCATCTATGAGGGCTATGCCCTGCCCCATGCCATCATGCGCCTTGATCTGGCTGGCCACGACCTCACGGACTAC
CTCATGAAGATCCTCACAGAAAGAGGCTATTCCTTTGTGACCACAGCTGAGTAAGAAATCGGGTGAGACATCAAGGAGAA
ACTGTGCTATGTGGCCCTGGATTTTGAGAATGAGATGGCCACAGCCTCCTCTTTCTCTCTGGAGAAGAGCTATGAGCTAC
CAGATGGGCAAGTCATCACCATTGGCAAAGAGAGCTTCCGCTGCCCCAAGACCCTCTTCCAGCCTTCCTTCATTGGTATG
GAGTCCGCGGGAATTCATGAGACAACCTACAGTTCCATCATGAAGTGTGACACTGATATCTGTAAGGACTTATATGCCAA
CAATGTCCTCTCTGGGGGCACCACCATGTATCCTGGCATTGCTGGCAGGATGCAGAAGGAGATCACAGCCCTGGCCCCCA
GTACCATGAAGATCAAGATTATTGCTCCCCCAGAGCGGAAGTGCTCAGTGTGGATCGGGGGTTCTCTTCTGGCCTCTCTC
TCCACCTTCCAGCAGATGTGGATCAGCAAGCCTGAGGATGATGAAGCAGGGCCCTCCATTGTCCACAGGAAGTGCTTT

Alignment

ORF - retro_tsyr_858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEDSTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
          E...T.L.CD..SGLCKAGFAG.DA.RAVFPSIVG.PRHQGVMVG.GQKDSYVGDEAQSKRGILTLKYPI
Retrocopy EDEATTLMCDHDSGLCKAGFAGYDALRAVFPSIVGHPRHQGVMVGRGQKDSYVGDEAQSKRGILTLKYPI

Parental  EHGIITNWDDMEKIWHHSLYNELRVAPEEHPTLLTEAP-LNPKANREKMTQIMFETFNVPAMYVAIQAVL
          EHGII.NWDDMEKIWHHS.YNEL.VAPEEHPTLLTEAP.LNPKANREKMTQIMFETFNVPAMYVAIQA..
Retrocopy EHGIIINWDDMEKIWHHSFYNELHVAPEEHPTLLTEAP<LNPKANREKMTQIMFETFNVPAMYVAIQAMF

Parental  SLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVR
          SLYASGRT.G.VLDSG.GVT.NVPIYEGYALPHAIMRLDLAG.DLTDYLMKILTERGYSFVTTAE.EI..
Retrocopy SLYASGRTAGVVLDSGNGVTPNVPIYEGYALPHAIMRLDLAGHDLTDYLMKILTERGYSFVTTAE*EIG*

Parental  DIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYN
          DIKEKLCYVALDFENEMATA.SS.SLEKSYELPDGQVITIG.E.FRCP.TLFQPSFIGMESAGIHETTY.
Retrocopy DIKEKLCYVALDFENEMATA-SSFSLEKSYELPDGQVITIGKESFRCPKTLFQPSFIGMESAGIHETTYS

Parental  SIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLS
          SIMKCD.DI.KDLYANNVLSGGTTMYPGIA.RMQKEITALAPSTMKIKIIAPPERK.SVWIGGS.LASLS
Retrocopy SIMKCDTDICKDLYANNVLSGGTTMYPGIAGRMQKEITALAPSTMKIKIIAPPERKCSVWIGGSLLASLS

Parental  TFQQMWISKQEYDEAGPSIVHRKCF
          TFQQMWISK.E.DEAGPSIVHRKCF
Retrocopy TFQQMWISKPEDDEAGPSIVHRKCF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_858 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000759	3 retrocopies	retro_chof_1909, retro_chof_2042, retro_chof_21,
Dasypus novemcinctus	ENSDNOG00000006719	1 retrocopy	retro_dnov_32,
Echinops telfairi	ENSETEG00000008526	1 retrocopy	retro_etel_41,
Macropus eugenii	ENSMEUG00000010843	1 retrocopy	retro_meug_1374,
Myotis lucifugus	ENSMLUG00000015509	3 retrocopies	retro_mluc_190, retro_mluc_427, retro_mluc_90,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Pongo abelii	ENSPPYG00000002459	1 retrocopy	retro_pabe_3027,
Sorex araneus	ENSSARG00000005778	1 retrocopy	retro_sara_732,
Tupaia belangeri	ENSTBEG00000017616	3 retrocopies	retro_tbel_1555, retro_tbel_3014, retro_tbel_4616,
Tarsius syrichta	ENSTSYG00000000406	1 retrocopy	retro_tsyr_2031,
Tarsius syrichta	ENSTSYG00000008155	5 retrocopies	retro_tsyr_1282, retro_tsyr_2102, retro_tsyr_858 , retro_tsyr_9, retro_tsyr_92,
Vicugna pacos	ENSVPAG00000010621	3 retrocopies	retro_vpac_12, retro_vpac_355, retro_vpac_651,