RetrogeneDB ID: retro_tbel_1503

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4903:41416..42225(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HCCS
• Ensembl ID: ENSTBEG00000002670
• Aliases: None
• Description: holocytochrome c synthase [Source:HGNC Symbol;Acc:4837]

Sequence

>retro_tbel_1503
ATTAGTTTGTCTGCATCTACTCCTCCTGTTGCAGTTCAGACCTCAGATCATCAGATCGTCAAAGAGCATCCCCACCTAAT
GGATGCCCAACACATGAAGGGAAGATGAGGCTGTCCACTGAGCATGCAACCATCCGACCCAACCTGTGAGAGTAAAAAGT
ACTCTGTACCTGCCCACCAGGACCACACATACGTGTATGTGGAGTGTCCCATCATGGGTACCATGGCTGGAAAGGAGAAT
TTAGATCCTTCAAATCTGATGCCACCACCTAATCAAACACCAGCCCCAGATCAGCCATTTGCACTGTCTACTGTCCGAGA
GGAGTCTCCCATTCCGAGAGTAGATTCAGAAAGAAGTGGATTTATCCTTCTGAGCAAATGTTCTGGAATGCAATGTTAAG
GAAAGGGTGAAAGTGGAAGGAGGAGGGCATCAGTCAAAAAGGCAAGTATAATATCATTAAAATTCATAATCAGAATAATG
AGCAGGCTTGGAAGGAGATTTTGAAGTGGGAAGCCCTTCATGCCAAGGAGTGCCCATGTGGCCCATCCTTTATCCGGTTT
GAAGGGAAGGCAAAAGAGCATTCACCAAGGGCACGAATTTGCTCATGGATGGGGTATGAGTTGACTTTTGATAGGCACGA
TTGGGTCATTGACCACTGTGGGACAGAAGTTAGATACGTCATTGATTACTACGATGGCAGTGAAGTCAACAAGGACTATC
AGTTCACCATCCTGGATGTCCGTCCCGCCTTGGATTCACTTTCAGCAGTATGGGACAGAATGAAGCTTGCTTGGTGGCGC
TGAACTTCG

Alignment

ORF - retro_tbel_1503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGLSASTPVAVQTSNASDHQRASPPSGCPMHEGKIKGCPVSMEPSDPSCESKKYSVPAHQDRAYEYVECP
          ..LSASTP...............P......H.....GCP.SM.PSDP.CESKKYSVPAHQD..Y.YVECP
Retrocopy ISLSASTPPVAVQTSDHQIVKEHPHLMDAQHMKGR*GCPLSMQPSDPTCESKKYSVPAHQDHTYVYVECP

Parental  VTGAMAGKENLDPSNLMPPPNQTPAPDQPFALSTVREESSIPRADSE-KKWVYPSEQMFWNAMLRKGWKW
          ..G.MAGKENLDPSNLMPPPNQTPAPDQPFALSTVREES.IPR.DSE.KKW.YPSEQMFWNAMLRKG.KW
Retrocopy IMGTMAGKENLDPSNLMPPPNQTPAPDQPFALSTVREESPIPRVDSE<KKWIYPSEQMFWNAMLRKG*KW

Parental  KEEDISQKDMYNIIKIHNQNNEQAWKEILKWEALHAKECPCGPSLIRFGGKAKEYSPRARIRSWMGYELP
          KEE.ISQK..YNIIKIHNQNNEQAWKEILKWEALHAKECPCGPS.IRF.GKAKE.SPRARI.SWMGYEL.
Retrocopy KEEGISQKGKYNIIKIHNQNNEQAWKEILKWEALHAKECPCGPSFIRFEGKAKEHSPRARICSWMGYELT

Parental  FDRHDWIVDRCGTEVRYVIDYYDGGEVNKDYQF-ILDVRPALDSLSAVWDRMKVAWWRWTS
          FDRHDW..D.CGTEVRYVIDYYDG.EVNKDYQF.ILDVRPALDSLSAVWDRMK.AWWR.TS
Retrocopy FDRHDWVIDHCGTEVRYVIDYYDGSEVNKDYQFTILDVRPALDSLSAVWDRMKLAWWR*TS

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_1503 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1503 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022393	1 retrocopy	retro_fcat_1706,
Myotis lucifugus	ENSMLUG00000003569	1 retrocopy	retro_mluc_1621,
Ictidomys tridecemlineatus	ENSSTOG00000014037	6 retrocopies	retro_itri_1277, retro_itri_1462, retro_itri_1594, retro_itri_1700, retro_itri_242, retro_itri_745,
Tupaia belangeri	ENSTBEG00000002670	1 retrocopy	retro_tbel_1503 ,