RetrogeneDB ID: retro_tbel_4185

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_70776:3608..4381(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000011817
• Aliases: None
• Description: None

Sequence

>retro_tbel_4185
AATTCTTTGCCTGAGCCTATTTTGGTTGATACTTCTCCAAGCCCAATGGAAACATCTGGATGTGCTCCTGCAGAAAGATA
TCTGTGTGAGGCTTTCTCTGATGTAATTCTTGCAGTGAGTGATGTGGACCCAGAAGATGGAGCTGATCCAAACCTTTGCA
GTGAATATGTAAAAGATACCTGTGCTTATCTGAGATAGCTCGAGGAAGAGCAAGCAGTCAGACCAAAATACCTACTGGGT
TGGGAAATCACTGGAAACATGAGAGCCATCCTAATTGACTGGGTAGTACAGGTTCAAATGAAATTCTGGTTGCTGCAGGA
GGCCAAGTATATGACTGTTTCTATTATTGATTGATCCATGCGGAATAATTGTGTGCTCAAGAAGATGCTGCAGTTGGTTG
GTGTCACTGCCATGTTTGTTGCAAGCAAGTATGAGGAAATGTGCCCCACCCCCCCGAAGTTGGTGACTTTGCTTTTGCAA
CTAACAATACTTACACTAAGCATCAAATCAGGCAGATGGAAATGAAGAGTCTAAGAGTTTTAAACTTTGGTCTGGGTCGT
CCTCTATCCCTGCTCTTTCTTCAGCAAGCATTTAAAGTTGGAGAGGTCAATGTTGAACAACATACTCTGGCCAAGCACCT
GATGGAATTAACTATGCTTGATTATGATATGGTGCACTCTCCTCCTTCTCAAATTGCAGCAGGAGATTTTTGCCTAGCCC
TGAAAATTCTTGATAATGGTGAACGGACACCAACTCTCCAGTATTACATTACA

Alignment

ORF - retro_tbel_4185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NSSPEPILVDTSSSSPMETSGCAPAEEYLCQAFSDVILAVSDVDAEDGADPNLCSEYVKDIYAYLRQLEE
          NS.PEPILVDTS.S.PMETSGCAPAE.YLC.AFSDVILAVSDVD.EDGADPNLCSEYVKD..AYLR.LEE
Retrocopy NSLPEPILVDTSPS-PMETSGCAPAERYLCEAFSDVILAVSDVDPEDGADPNLCSEYVKDTCAYLR*LEE

Parental  EQAVRPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQETMYMTVSIIDRFMQNNCVPKKMLQLVGVTAMF
          EQAVRPKYLLG.E.TGNMRAILIDW.VQVQMKF.LLQE..YMTVSIID..M.NNCV.KKMLQLVGVTAMF
Retrocopy EQAVRPKYLLGWEITGNMRAILIDWVVQVQMKFWLLQEAKYMTVSIID*SMRNNCVLKKMLQLVGVTAMF

Parental  IASKYEEM--YPPEI-GDFAFVTNNTYTKHQIRQMEMKILRALNFGLGRPLPLHFLRRASKVGEVDVEQH
          .ASKYEEM...PP...GDFAF.TNNTYTKHQIRQMEMK.LR.LNFGLGRPL.L.FL..A.KVGEV.VEQH
Retrocopy VASKYEEMCPTPPKL<GDFAFATNNTYTKHQIRQMEMKSLRVLNFGLGRPLSLLFLQQAFKVGEVNVEQH

Parental  TLAKYLMELTMLDYDMVHFPPSQIAAGAFCLALKILDNGEWTPTLQHYLS
          TLAK.LMELTMLDYDMVH.PPSQIAAG.FCLALKILDNGE.TPTLQ.Y..
Retrocopy TLAKHLMELTMLDYDMVHSPPSQIAAGDFCLALKILDNGERTPTLQYYIT

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_4185 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4185 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 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014239	2 retrocopies	retro_btau_1317, retro_btau_600,
Canis familiaris	ENSCAFG00000007705	1 retrocopy	retro_cfam_213,
Callithrix jacchus	ENSCJAG00000016075	1 retrocopy	retro_cjac_4137,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Erinaceus europaeus	ENSEEUG00000005724	2 retrocopies	retro_eeur_386, retro_eeur_548,
Felis catus	ENSFCAG00000001572	1 retrocopy	retro_fcat_840,
Myotis lucifugus	ENSMLUG00000012856	1 retrocopy	retro_mluc_1020,
Mustela putorius furo	ENSMPUG00000014648	1 retrocopy	retro_mputfur_58,
Mus musculus	ENSMUSG00000041431	5 retrocopies	retro_mmus_1170, retro_mmus_1550, retro_mmus_2508, retro_mmus_2615, retro_mmus_3023,
Procavia capensis	ENSPCAG00000002451	1 retrocopy	retro_pcap_176,
Rattus norvegicus	ENSRNOG00000018635	2 retrocopies	retro_rnor_568, retro_rnor_814,
Sarcophilus harrisii	ENSSHAG00000007685	1 retrocopy	retro_shar_290,
Tupaia belangeri	ENSTBEG00000011817	4 retrocopies	retro_tbel_1185, retro_tbel_3200, retro_tbel_4185 , retro_tbel_4531,
Tarsius syrichta	ENSTSYG00000008928	1 retrocopy	retro_tsyr_232,
Tursiops truncatus	ENSTTRG00000002874	2 retrocopies	retro_ttru_524, retro_ttru_59,