RetrogeneDB ID: retro_tbel_1410

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4622:40191..40905(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000002163
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MKRN1
• Ensembl ID: ENSTBEG00000004564
• Aliases: None
• Description: makorin ring finger protein 1 [Source:HGNC Symbol;Acc:7112]

Sequence

>retro_tbel_1410
AAAGCCCCCCTTGCTGCATCCTCTGGCTCCTTGCCTCTGATTGGCTCGGCTGCTGACAGGAGCTCTTTTGAAGCCGAGAC
CCACAGTGCAGGCGGTGAAGTTGCTGGAGGAGCAGGTGCAGAGGGCTGGGAGGATGCTGTGGAGTTTGTTCCCGGACAGC
CCTACCGGGGCCGCAGGGTCCCTTCCGTCCCTCAGGCTCCTCCACAGAGCTCGGTGGCTGAGAGCGAGCAGATGGCTGTG
GGCGCCAGGGAGCAGCTTTGTCCCTATGCTGCCAGGGGACAGTGCTTTCGTGGTGAGAGCTGTGAGTACCTCCACGGAGA
CACGTGCGACATGTGTGGCCTGCAGGCCTTGCACCCTGTGGACGCTGCCCAGAGGGCAGACCACATCAGGGCCTGCATCG
AAGCGCATGAGAAAGACATGGAGCTGTCGTTTGCCGTGCAGCGCAGCGCAGACAAGGTGTGCGGCATCTGCATGGAGGTG
GTCTATGAGAAAGCCAACCCTGGCGACTGCCGCTTTGGCATCCTTTCCAACTGCAACCACACCTTCTGCCTTAAGTGTAT
CCGCAGGTGGAGGAGTGCCAGACAATTTGAGAACAGGATCATTAAGTCCTGCCCACAGTGCAGGGTCACCTCCAACTTCG
TCATCCCCAGCCAGTTCTGGGTGGAGGAGGAGGAGGAGAAGCAGAAGCTCATTCAGCAGTACAAGGAGGCCATG

Alignment

ORF - retro_tbel_1410 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.42 %
• Parental protein coverage: 79.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSSLAASS-SLPSVGPLGDMNTTEAESRNSS--FATGAGSEDWVNAIEFVPGQPYCGRTAPSCTEAPLQG
          K..LAASS.SLP..G...D....EAE........A.GAG.E.W..A.EFVPGQPY.GR..PS...AP.Q.
Retrocopy KAPLAASSGSLPLIGSAADRSSFEAETHSAGGEVAGGAGAEGWEDAVEFVPGQPYRGRRVPSVPQAPPQS

Parental  SVAKEESEKEPSAVETKKQLCPYAAVGECRYGENCVYLHGDACDMCGLQVLHPMDAAQRSQHIKSCIEAH
          SVA....E.E..AV....QLCPYAA.G.C..GE.C.YLHGD.CDMCGLQ.LHP.DAAQR..HI..CIEAH
Retrocopy SVA----ESEQMAVGAREQLCPYAARGQCFRGESCEYLHGDTCDMCGLQALHPVDAAQRADHIRACIEAH

Parental  EKDMELSFAVQRSKDMVCGICMEVVYEKANPSERRFGILSNCNHTYCLKCIRKWRSAKQFESKIIKSCPE
          EKDMELSFAVQRS.D.VCGICMEVVYEKANP...RFGILSNCNHT.CLKCIR.WRSA.QFE..IIKSCP.
Retrocopy EKDMELSFAVQRSADKVCGICMEVVYEKANPGDCRFGILSNCNHTFCLKCIRRWRSARQFENRIIKSCPQ

Parental  CRITSNFVIPSEYWVEEKEEKQKLIQKYKEAM
          CR.TSNFVIPS..WVEE.EEKQKLIQ.YKEAM
Retrocopy CRVTSNFVIPSQFWVEEEEEKQKLIQQYKEAM

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_1410 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1410 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008306	2 retrocopies	retro_btau_401, retro_btau_943,
Canis familiaris	ENSCAFG00000003953	2 retrocopies	retro_cfam_2157, retro_cfam_253,
Callithrix jacchus	ENSCJAG00000013474	2 retrocopies	retro_cjac_210, retro_cjac_2991,
Cavia porcellus	ENSCPOG00000000948	1 retrocopy	retro_cpor_109,
Gorilla gorilla	ENSGGOG00000023977	4 retrocopies	retro_ggor_119, retro_ggor_2813, retro_ggor_3031, retro_ggor_381,
Macaca mulatta	ENSMMUG00000010420	3 retrocopies	retro_mmul_191, retro_mmul_2597, retro_mmul_76,
Ochotona princeps	ENSOPRG00000010353	1 retrocopy	retro_opri_1073,
Procavia capensis	ENSPCAG00000014683	1 retrocopy	retro_pcap_19,
Pongo abelii	ENSPPYG00000018057	3 retrocopies	retro_pabe_3435, retro_pabe_3776, retro_pabe_947,
Tupaia belangeri	ENSTBEG00000004564	2 retrocopies	retro_tbel_1410 , retro_tbel_71,