RetrogeneDB ID: retro_tbel_428

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2044:244707..245272(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL35
• Ensembl ID: ENSTBEG00000015366
• Aliases: None
• Description: mitochondrial ribosomal protein L35 [Source:HGNC Symbol;Acc:14489]

Sequence

>retro_tbel_428
GTGGCGGCCTCCACCTTTGCTGGAGCTGTGCAAGCAGCTTCAGGAATCTTACAGCCCCTTAATATTTTGGCTTCTTCAAT
GTATCACAATTGTGCCAAGAATGCCTGTCTGTCTTCTGCACTGTCCACCGGACATTTCAGTCAGATTCAGACACCAGTTG
TTCCCTCTGCTCCTAGATGTCTCGCAGCTGTTAGAGACCTGACATGTGGCCGTACTGCAATGATCCTTAGCAGAGCGGCA
CCCTTGTTTCCAGGTGTCCTGAAGCTGCCCCCAGTCAGAACCGTAACACACGTCAGTTCACGGAAAGGCAAGAGGAAGAC
TGTGAAGGCTGTCATCTACAGGTTTCTTCGGCTTCATTCTGGCCTTTGGCTAAGGAGAAAGGCTGGTTATAAGAAAAAAT
TATGGAGAAAGGAAAACACAAGAAAAAAACGCTTGAGGGAATTTGTGTTCTGCAATAAAACCCAAAACAAATTCTTGATA
AAATGACAACATCTTCCTGGAAGAGGCGAAACTGATATGTTGCTGATCCTTCCAGAAGTATCATGATCCCACAAACCTGA
AAGTA

Alignment

ORF - retro_tbel_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAASVFAGAVRATSGILRPLSILASSAYRNCAQNACLSSALSTRHFSHIQTPVVSSAPRFLTAVGDLTRG
          .AAS.FAGAV.A.SGIL.PL.ILASS.Y.NCA.NACLSSALST.HFS.IQTPVV.SAPR.L.AV.DLT.G
Retrocopy VAASTFAGAVQAASGILQPLNILASSMYHNCAKNACLSSALSTGHFSQIQTPVVPSAPRCLAAVRDLTCG

Parental  RTATILNRVAPLLPDVLKLPPVRTVTYVSTRKGKRKTVKAVIYRFLRLHSGLWLRRKAGYKKKLWKKDNA
          RTA.IL.R.APL.P.VLKLPPVRTVT.VS.RKGKRKTVKAVIYRFLRLHSGLWLRRKAGY..........
Retrocopy RTAMILSRAAPLFPGVLKLPPVRTVTHVSSRKGKRKTVKAVIYRFLRLHSGLWLRRKAGYXXXXXXXXXX

Parental  RKKRLREFVFCNKTQSK-LLDKMTTSFWKRRNWYADDP-YQKYHDRTNLKV
          ...RLREFVFCNKTQ.K..LDKMTTS.WKRRN.Y..DP..QKYHD.TNLKV
Retrocopy XXXRLREFVFCNKTQNK<ILDKMTTSSWKRRN*YVADP<FQKYHDPTNLKV

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_428 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_428 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 13 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019467	1 retrocopy	retro_cjac_203,
Dasypus novemcinctus	ENSDNOG00000008329	1 retrocopy	retro_dnov_404,
Homo sapiens	ENSG00000132313	4 retrocopies	retro_hsap_3424, retro_hsap_4784, retro_hsap_595, retro_hsap_681,
Gorilla gorilla	ENSGGOG00000026769	3 retrocopies	retro_ggor_2315, retro_ggor_2979, retro_ggor_526,
Macropus eugenii	ENSMEUG00000004773	1 retrocopy	retro_meug_1703,
Mus musculus	ENSMUSG00000052962	1 retrocopy	retro_mmus_1777,
Nomascus leucogenys	ENSNLEG00000002756	4 retrocopies	retro_nleu_1103, retro_nleu_1362, retro_nleu_2217, retro_nleu_781,
Otolemur garnettii	ENSOGAG00000004048	1 retrocopy	retro_ogar_2600,
Pongo abelii	ENSPPYG00000012214	5 retrocopies	retro_pabe_1817, retro_pabe_2837, retro_pabe_3724, retro_pabe_541, retro_pabe_595,
Pan troglodytes	ENSPTRG00000012152	4 retrocopies	retro_ptro_2325, retro_ptro_3185, retro_ptro_438, retro_ptro_489,
Rattus norvegicus	ENSRNOG00000008546	1 retrocopy	retro_rnor_1399,
Tupaia belangeri	ENSTBEG00000015366	10 retrocopies	retro_tbel_1143, retro_tbel_146, retro_tbel_2647, retro_tbel_289, retro_tbel_2892, retro_tbel_3789, retro_tbel_3828, retro_tbel_428 , retro_tbel_4379, retro_tbel_627,
Tarsius syrichta	ENSTSYG00000007713	2 retrocopies	retro_tsyr_1128, retro_tsyr_264,