RetrogeneDB ID: retro_tbel_1462

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4790:308943..309437(-)
• Located in intron of: ENSTBEG00000008354

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEA1
• Ensembl ID: ENSTBEG00000012294
• Aliases: None
• Description: male-enhanced antigen 1 [Source:HGNC Symbol;Acc:6986]

Sequence

>retro_tbel_1462
AGGCTCTGAGTAGCCCCTACCTAGATGGTGGCAATAGTTCTAGCGGGAGACACCATGGGCCCTGAGCAAATCTTCCCAAT
CAGACTGAGGAACTAAAGTCTCATCAGGGTCTCACAGAGGTACTGGGGTTAGAGCATTGAGGAACCTGAGAGAAAGCAGG
AGGAAATGAGGCCAGGCCCAGCTCACTTCCACCAGCCCCGGAACTAAGATCCTGAACAAGAGGAGCTGGAGCAGGCACCA
GTGGATCATGAAGATAGTGAAGTTGCTGACATCCAGGGTTGGATCCAGGCCTTGAGTTTCATTTGTCAGACCTGCCATTA
AAGAGTGAGGATGAATAGGAAGGGTATTGCATTGAGCAATCACGGCTCTATTTCCACAGACCCAGAAATCACAGAGCTGG
TGAAAATGACACAGGTGGAATAGCACCAGTTCTGTCTGTGCAAGGGCTTCCTTCCTGGGATCAGGAGATATCAAATGCAC
AACGGGATGATATG

Alignment

ORF - retro_tbel_1462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.29 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RLSGAPARMAAVVLGRDTMGPERIFP-NQTEELGPHQGPAE-GTG-DWSSEEPEEEQEDTGAGPAGYSYQ
          RL..AP..M.A.VL..DTMGPE.IFP.NQTEEL..HQG..E.GTG...S.EEPE..QE....GPA....Q
Retrocopy RL*VAPT*MVAIVLAGDTMGPEQIFP<NQTEELKSHQGLTE<GTG<G*SIEEPERKQEEMRPGPAHF-HQ

Parental  PLNQDPEQEEVELAPVGDGEDVVGDIQDRIQALGL-HLPDPPIESEDEDE-EGATALSNHSSIPMDPEHV
          P.N.DPEQEE.E.APV......V.DIQ..IQAL...HL.D.P..S..EDE.....ALSNH.SI..DPE..
Retrocopy PRN*DPEQEELEQAPVDHEDSEVADIQGWIQALSF<HLSDLPLKS--EDE>RKGIALSNHGSISTDPEIT

Parental  ELVKRTM-AGVS--LPAPGVPAWAREISDAQWEDV
          ELVK.T...G....L...G.P.W..EIS.AQ..D.
Retrocopy ELVKMTQ<GGIAPVLSVQGLPSWDQEISNAQRDDM

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_1462 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1462 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012655	1 retrocopy	retro_amel_1620,
Bos taurus	ENSBTAG00000005536	1 retrocopy	retro_btau_240,
Canis familiaris	ENSCAFG00000001756	1 retrocopy	retro_cfam_1643,
Callithrix jacchus	ENSCJAG00000004894	2 retrocopies	retro_cjac_2054, retro_cjac_824,
Cavia porcellus	ENSCPOG00000022111	1 retrocopy	retro_cpor_1530,
Echinops telfairi	ENSETEG00000002439	1 retrocopy	retro_etel_236,
Felis catus	ENSFCAG00000031337	1 retrocopy	retro_fcat_1772,
Loxodonta africana	ENSLAFG00000013881	1 retrocopy	retro_lafr_60,
Myotis lucifugus	ENSMLUG00000012138	2 retrocopies	retro_mluc_1819, retro_mluc_851,
Monodelphis domestica	ENSMODG00000019002	1 retrocopy	retro_mdom_878,
Oryctolagus cuniculus	ENSOCUG00000001565	2 retrocopies	retro_ocun_1312, retro_ocun_1446,
Pelodiscus sinensis	ENSPSIG00000002330	1 retrocopy	retro_psin_56,
Pteropus vampyrus	ENSPVAG00000008711	1 retrocopy	retro_pvam_266,
Rattus norvegicus	ENSRNOG00000017144	2 retrocopies	retro_rnor_716, retro_rnor_961,
Tupaia belangeri	ENSTBEG00000012294	2 retrocopies	retro_tbel_1462 , retro_tbel_3528,
Tursiops truncatus	ENSTTRG00000006996	1 retrocopy	retro_ttru_357,