RetrogeneDB ID: retro_tbel_4652

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_96460:10131..10938(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CS
• Ensembl ID: ENSTBEG00000006425
• Aliases: None
• Description: citrate synthase [Source:HGNC Symbol;Acc:2422]

Sequence

>retro_tbel_4652
CTGATTTACCAAGACTCTATGGATCTGATCGCGAAGCTACCTTATGTTGCAGCGAAGATCTACCGGAATCTACCAGGAGG
GCAGCAGTATTGGGGCTATTGACTCTAAGCTGGACTGGTCTCACAATTTCACCAACATGTTAGGCTATACTGATGCTCAG
TTCACTGAGCTCATGTGCTTGTACCTCACCATTCACAGTGATGATGAAGGCGGCAGCGTAAGTGCCCATACCAGCCACTT
GGTGGGCAGTGCCCTTTCAGGCCCTTACCTGTCCTTTGCAGCAGCCATGAATGGGCTGGCAGGGCCTCTACATGGATTAG
CAAATCAGGAAGTGCTTGTCTGGCTAACACAACTACAGAGGAAGTTGGCAAAGATGTGTTAGATGAGAAGTTGCGAGACT
ACATCTGGAACACACTCAACTCAGGATGGGTTGTCCCAGGCTATGGCCATGCAGTACTAAGGAAGACTGATCCACGATAT
ACCTGTCAGCAGGAGTTTGCTCTGAAACACCTGCCTAATGACCCCCCGTTTAAGCTGGTTGCTCAGCTGTACAAGATAGT
GCCCAATATGCTTTTAGAGCAGGGCAAAGCCAAGAATCCTTAGCCCAATGTTGACGTTGATAGTGGGGTGCTGCTCCAGT
ACTATGGCATGACGGAGATGAATTACTACACAGCCCTGTTTGGGGTGTCACGGGCCCTGGGTGTACTGGCGCAGCTCATC
TGGAGCCGAGCCCTAGGTTTCCCTCTAGAAAGGCCCAAATCCATGAGCACGGATGATCTGATGAAGTTTGTGGGCCCTAA
GTCAGGG

Alignment

ORF - retro_tbel_4652 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.38 %
• Parental protein coverage: 57.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LIYEDCMDLIAKLPCVAAKIYRNL-YREGSSIG-AIDSKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSD
          LIY.D.MDLIAKLP.VAAKIYRNL..R.....G.AIDSKLDWSHNFTNMLGYTDAQFTELM.LYLTIHSD
Retrocopy LIYQDSMDLIAKLPYVAAKIYRNL<TRRAAVLG<AIDSKLDWSHNFTNMLGYTDAQFTELMCLYLTIHSD

Parental  HEGGNVSAHTSHLVGSALSDPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQK-EVGKDVSDEKLRDYIW
          .EGG.VSAHTSHLVGSALS.PYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQ..EVGKDV.DEKLRDYIW
Retrocopy DEGGSVSAHTSHLVGSALSGPYLSFAAAMNGLAGPLHGLANQEVLVWLTQLQR<EVGKDVLDEKLRDYIW

Parental  NTLNSGRVVPGYGHAVLRKTDPRYTCQREFALKHLPNDPLFKLVAQLYKIVPNILLEQGKAKNPWPNVDA
          NTLNSG.VVPGYGHAVLRKTDPRYTCQ.EFALKHLPNDP.FKLVAQLYKIVPN.LLEQGKAKNP.PNVD.
Retrocopy NTLNSGWVVPGYGHAVLRKTDPRYTCQQEFALKHLPNDPPFKLVAQLYKIVPNMLLEQGKAKNP*PNVDV

Parental  HSGVLLQYYGMTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLMKFVDSKSG
          .SGVLLQYYGMTEMNYYT.LFGVSRALGVLAQLIWSRALGFPLERPKSMSTD.LMKFV..KSG
Retrocopy DSGVLLQYYGMTEMNYYTALFGVSRALGVLAQLIWSRALGFPLERPKSMSTDDLMKFVGPKSG

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4652 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4652 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 21 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004371	1 retrocopy	retro_btau_386,
Canis familiaris	ENSCAFG00000000115	1 retrocopy	retro_cfam_765,
Choloepus hoffmanni	ENSCHOG00000000397	1 retrocopy	retro_chof_1803,
Callithrix jacchus	ENSCJAG00000011275	1 retrocopy	retro_cjac_2031,
Dasypus novemcinctus	ENSDNOG00000010907	2 retrocopies	retro_dnov_205, retro_dnov_468,
Echinops telfairi	ENSETEG00000012035	1 retrocopy	retro_etel_584,
Homo sapiens	ENSG00000062485	2 retrocopies	retro_hsap_1972, retro_hsap_3621,
Gorilla gorilla	ENSGGOG00000009096	2 retrocopies	retro_ggor_1432, retro_ggor_2445,
Macropus eugenii	ENSMEUG00000005657	2 retrocopies	retro_meug_1078, retro_meug_1304,
Microcebus murinus	ENSMICG00000017659	2 retrocopies	retro_mmur_1322, retro_mmur_394,
Macaca mulatta	ENSMMUG00000002483	2 retrocopies	retro_mmul_1502, retro_mmul_1840,
Mus musculus	ENSMUSG00000005683	1 retrocopy	retro_mmus_258,
Nomascus leucogenys	ENSNLEG00000017514	2 retrocopies	retro_nleu_1201, retro_nleu_809,
Oryctolagus cuniculus	ENSOCUG00000007216	1 retrocopy	retro_ocun_1183,
Pongo abelii	ENSPPYG00000004654	1 retrocopy	retro_pabe_2972,
Rattus norvegicus	ENSRNOG00000023520	1 retrocopy	retro_rnor_2518,
Sorex araneus	ENSSARG00000010093	2 retrocopies	retro_sara_360, retro_sara_628,
Sus scrofa	ENSSSCG00000021091	1 retrocopy	retro_sscr_321,
Sus scrofa	ENSSSCG00000022858	1 retrocopy	retro_sscr_322,
Tupaia belangeri	ENSTBEG00000006425	1 retrocopy	retro_tbel_4652 ,
Tarsius syrichta	ENSTSYG00000004483	1 retrocopy	retro_tsyr_1659,