RetrogeneDB ID: retro_chof_104

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1992:155588..156033(-)
• Located in intron of: ENSCHOG00000001293

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSCHOG00000012728
• Aliases: None
• Description: transmembrane emp24 domain trafficking protein 2 [Source:HGNC Symbol;Acc:16996]

Sequence

>retro_chof_104
GGCTACTTGGACATCGACATAAAGATTACAGGGCCTGACAGTAAAGGAATTTATAAAGGATACCAAGGGTCCAGTGGAAA
ATACACATTTGCTGCTAACATGAATGGAACATACAAGTTTCGTATTAGCAATAGGTTGTCCACCATGACGCCAAAGAAAG
TGATGTTCACCATTGATGTTGGGGAGGTCCCAAAAGGACAAGACATGGAAACAAGCTCACCAGAACAAGCTAGAAGAAAT
GATCAATGAGCTAGCAATGGTGATGACAGCTGTAAAGCATGAACAGCAGTATATGAGAGTTTGGGAGAGAATACACAGAG
TAATCAATGACAACACAAACAGCAGAGTGGTCCTTTGGTCCTTCTTTGAAGCTCTTGTTCTAGTTGCCATGACATTGGGA
CAGATCTACTACCTGAAGAGAGTTTTTGAAGTCCCGAGGGTTGTT

Alignment

ORF - retro_chof_104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 73.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFLDIDVE---PDNKGIYKGDRESSGKYTFAAHMDGTYKFCFSNRMSTMTPKIVMFTIDI-GEAPKGQDM
          G.LDID.....PD.KGIYKG...SSGKYTFAA.M.GTYKF..SNR.STMTPK.VMFTID..G...K....
Retrocopy GYLDIDIKITGPDSKGIYKGYQGSSGKYTFAANMNGTYKFRISNRLSTMTPKKVMFTIDV>GRSQKDKTW

Parental  ETEAHQNKLEEMINELAVAMTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSFFEALVLVAMTLGQIYYL
          ...AHQNKLEEMINELA..MTAVKHEQ.YM.V.ERIHR.INDNTNSRVVLWSFFEALVLVAMTLGQIYYL
Retrocopy K-QAHQNKLEEMINELAMVMTAVKHEQQYMRVWERIHRVINDNTNSRVVLWSFFEALVLVAMTLGQIYYL

Parental  KRFFEVRRVV
          KR.FEV.RVV
Retrocopy KRVFEVPRVV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_104 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015262	2 retrocopies	retro_amel_1923, retro_amel_337,
Bos taurus	ENSBTAG00000039630	2 retrocopies	retro_btau_52, retro_btau_819,
Choloepus hoffmanni	ENSCHOG00000012728	6 retrocopies	retro_chof_104 , retro_chof_1277, retro_chof_2323, retro_chof_2601, retro_chof_2709, retro_chof_981,
Callithrix jacchus	ENSCJAG00000020466	1 retrocopy	retro_cjac_1392,
Echinops telfairi	ENSETEG00000000556	2 retrocopies	retro_etel_2109, retro_etel_2154,
Homo sapiens	ENSG00000086598	1 retrocopy	retro_hsap_2793,
Gorilla gorilla	ENSGGOG00000028536	1 retrocopy	retro_ggor_1943,
Macaca mulatta	ENSMMUG00000031491	2 retrocopies	retro_mmul_1439, retro_mmul_613,
Mustela putorius furo	ENSMPUG00000001598	1 retrocopy	retro_mputfur_1241,
Mus musculus	ENSMUSG00000029390	2 retrocopies	retro_mmus_1361, retro_mmus_3262,
Nomascus leucogenys	ENSNLEG00000001652	2 retrocopies	retro_nleu_2454, retro_nleu_2794,
Otolemur garnettii	ENSOGAG00000009192	1 retrocopy	retro_ogar_2548,
Pongo abelii	ENSPPYG00000005090	3 retrocopies	retro_pabe_1919, retro_pabe_2227, retro_pabe_3597,
Tursiops truncatus	ENSTTRG00000007249	7 retrocopies	retro_ttru_1369, retro_ttru_1592, retro_ttru_1750, retro_ttru_1815, retro_ttru_216, retro_ttru_43, retro_ttru_615,