RetrogeneDB ID: retro_tsyr_644

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_159298:3218..3949(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000013840
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5B
• Ensembl ID: ENSTSYG00000009962
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide [Source:HGNC Symbol;Acc:830]

Sequence

>retro_tsyr_644
TCAGGTGTTACCAACTTAAAAGATGTTACTTCCAAGTTAGCACTGGTGTATGATAAAATGAATAATCCCCCTAGTGCTCA
TGCCCAAGTAGCTCTGACTGGACTGACTGTGGCTGAATACTTCAGAGACCAAGGAGGTCAAGATGTACTGTTGTTTATTG
ATAATATCTTCCACTTCACTCAGGCTGGCTCAGAAGTGTCTGCCTTACTGGGCAGACTCCCCTCTGCTGTGGGCTATCAG
CCTACCCTGGCCACTGACATGGGTACTATGCAGGAAAGAATCACCACCACCAAGAAGGGCTCTATCACCTCTGTGCAGGC
TATCTATGTGCCTTCTGATGACTTGACTGATCCCACTCCTGACACGACCTTTGCCCACTTGGATGCAACCACTGTACTGT
CTCATGCTATTGCTGAGCTGGGCATCTATCCTGCTGTGGATCCTTTGGACTCCACCTCCTGCATCATGGATCCCAACATT
GTGGGCGCTGAGCATTATGACGGTGCCCGTGGGGTGCAAAAGATCCTGCAGGACTACAAATCCCTCCAGGACATCATTGC
CGTCCTAGGTATGGATGAACTGTCTGAGGAAGACAAGCTGACTGTGTCTCGTGCACAGAAAATGCAGCGTTTCTTATCTC
AGCCATTCCAGATTGCTGAGGTCTTCACAGGTCATATGGGAAAGCTGGTAGCCTGAAGGAGACCATCAAAGGATTCCAGC
AGATCTTGGCA

Alignment

ORF - retro_tsyr_644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.8 %
• Parental protein coverage: 54.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGVINLKDATSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALL
          SGV.NLKD.TSK.ALVY..MN.PP.A.A.VALTGLTVAEYFRDQ.GQDVLLFIDNIF.FTQAGSEVSALL
Retrocopy SGVTNLKDVTSKLALVYDKMNNPPSAHAQVALTGLTVAEYFRDQGGQDVLLFIDNIFHFTQAGSEVSALL

Parental  GRIPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAEL
          GR.PSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVP.DDLTDP.P.TTFAHLDATTVLS.AIAEL
Retrocopy GRLPSAVGYQPTLATDMGTMQERITTTKKGSITSVQAIYVPSDDLTDPTPDTTFAHLDATTVLSHAIAEL

Parental  GIYPAVDPLDSTSRIMDPNIVGTEHYDVARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVSRARKIQR
          GIYPAVDPLDSTS.IMDPNIVG.EHYD.ARGVQKILQDYKSLQDIIA.LGMDELSEEDKLTVSRA.K.QR
Retrocopy GIYPAVDPLDSTSCIMDPNIVGAEHYDGARGVQKILQDYKSLQDIIAVLGMDELSEEDKLTVSRAQKMQR

Parental  FLSQPFQVAEVFTGHMGKLV-PLKETIKGFQQILA
          FLSQPFQ.AEVFTGHMGKLV..LKETIKGFQQILA
Retrocopy FLSQPFQIAEVFTGHMGKLV<SLKETIKGFQQILA

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_644 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 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000016752	1 retrocopy	retro_acar_181,
Bos taurus	ENSBTAG00000013315	1 retrocopy	retro_btau_1264,
Choloepus hoffmanni	ENSCHOG00000005350	1 retrocopy	retro_chof_1544,
Dasypus novemcinctus	ENSDNOG00000011289	1 retrocopy	retro_dnov_361,
Echinops telfairi	ENSETEG00000010208	1 retrocopy	retro_etel_2162,
Macropus eugenii	ENSMEUG00000002875	6 retrocopies	retro_meug_1416, retro_meug_1608, retro_meug_411, retro_meug_430, retro_meug_685, retro_meug_908,
Macaca mulatta	ENSMMUG00000001027	1 retrocopy	retro_mmul_103,
Sus scrofa	ENSSSCG00000000405	1 retrocopy	retro_sscr_453,
Tarsius syrichta	ENSTSYG00000009962	1 retrocopy	retro_tsyr_644 ,
Tursiops truncatus	ENSTTRG00000002144	1 retrocopy	retro_ttru_371,
Vicugna pacos	ENSVPAG00000004025	2 retrocopies	retro_vpac_405, retro_vpac_562,