RetrogeneDB ID: retro_chof_1860

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_406707:76..632(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX1
• Ensembl ID: ENSCHOG00000011957
• Aliases: None
• Description: chromobox homolog 1 [Source:HGNC Symbol;Acc:1551]

Sequence

>retro_chof_1860
ATGGGGAAAAAACAAAACAAGAAGAAAGTGGAGGAGGTGCTAGAGGAAGAGCAAGAGGAATATGTGGTGGAAAAAGTTCT
CGACCGTCGAGTGGTAAAGGGCAAAGTGGAGTACCTCCTGAAGTGGAAGGGTTTTCTCAGATGAGGACAACACATGGGGA
GCCAGAAGGAACCTGGATTGCCCTGATCTCGTTGCTGAGTTTCCTGCAGTCACAGAAAACAGCACATGAGACAGATAAGT
CAGAGGGAGGCAAGCGCAAGCTGACTCTGATTCTGAAGATAAAGGAGAGGAGAGTAAACCAAAGAAGAAGAAAGAAGAGT
CAGAAAAGCCACGAGGCTTTGCCCGGGGTTTGGAGCCGGAGCGGATTATTGGAGCTACAGACTCCAGTGGAGAACTCATG
TTCCTGATGAAATGGAAAAACTCTGATGAGGCTGATCTGGTCCCTGCCAAGGAAGCCAATGTCAAGTGCCCACAGGTTGT
CATATCCTTCTATGAGGAAAGGCTGACGTGGCATTCCTATCCCTCAGAGGATGATGACAAAAAAGATGACAAGAAT

Alignment

ORF - retro_chof_1860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGKKQNKKKVEEVLEEEEEEYVVEKVLDRRVVKGKVEYLLKWKGF-SDEDNTWEPEENLDCPDLIAEF-L
          MGKKQNKKKVEEVLEEE.EEYVVEKVLDRRVVKGKVEYLLKWKGF.SDEDNTW....NLDCPDL.AEF.L
Retrocopy MGKKQNKKKVEEVLEEEQEEYVVEKVLDRRVVKGKVEYLLKWKGF>SDEDNTWGARRNLDCPDLVAEF>L

Parental  QSQKTAHETDKSEGGKRK-ADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMK
          QSQKTAHETDKSEGGKRK.ADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMK
Retrocopy QSQKTAHETDKSEGGKRK<ADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMK

Parental  WKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSEDDDKKDDKN
          WKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSEDDDKKDDKN
Retrocopy WKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSEDDDKKDDKN

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_1860 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 17 parental genes, and 92 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004890	2 retrocopies	retro_amel_1228, retro_amel_54,
Canis familiaris	ENSCAFG00000016832	1 retrocopy	retro_cfam_804,
Choloepus hoffmanni	ENSCHOG00000011957	2 retrocopies	retro_chof_1860 , retro_chof_2185,
Choloepus hoffmanni	ENSCHOG00000013843	22 retrocopies	retro_chof_1128, retro_chof_1147, retro_chof_1156, retro_chof_1178, retro_chof_1210, retro_chof_1223, retro_chof_132, retro_chof_1569, retro_chof_1672, retro_chof_1779, retro_chof_1863, retro_chof_1962, retro_chof_222, retro_chof_2269, retro_chof_2347, retro_chof_2379, retro_chof_2435, retro_chof_2695, retro_chof_411, retro_chof_676, retro_chof_87, retro_chof_936,
Callithrix jacchus	ENSCJAG00000007532	2 retrocopies	retro_cjac_191, retro_cjac_51,
Felis catus	ENSFCAG00000006056	1 retrocopy	retro_fcat_514,
Homo sapiens	ENSG00000108468	3 retrocopies	retro_hsap_4654, retro_hsap_4790, retro_hsap_4840,
Gorilla gorilla	ENSGGOG00000024063	3 retrocopies	retro_ggor_2887, retro_ggor_3019, retro_ggor_330,
Microcebus murinus	ENSMICG00000009510	4 retrocopies	retro_mmur_1324, retro_mmur_178, retro_mmur_467, retro_mmur_999,
Mustela putorius furo	ENSMPUG00000015302	1 retrocopy	retro_mputfur_1457,
Nomascus leucogenys	ENSNLEG00000002435	4 retrocopies	retro_nleu_1089, retro_nleu_1105, retro_nleu_1955, retro_nleu_2961,
Oryctolagus cuniculus	ENSOCUG00000008021	3 retrocopies	retro_ocun_177, retro_ocun_442, retro_ocun_55,
Procavia capensis	ENSPCAG00000002381	2 retrocopies	retro_pcap_134, retro_pcap_308,
Pongo abelii	ENSPPYG00000008891	1 retrocopy	retro_pabe_78,
Sarcophilus harrisii	ENSSHAG00000008192	1 retrocopy	retro_shar_76,
Sus scrofa	ENSSSCG00000017529	1 retrocopy	retro_sscr_635,
Tupaia belangeri	ENSTBEG00000014931	39 retrocopies	retro_tbel_1388, retro_tbel_1557, retro_tbel_1613, retro_tbel_1655, retro_tbel_1663, retro_tbel_1794, retro_tbel_2124, retro_tbel_2130, retro_tbel_2281, retro_tbel_2313, retro_tbel_2346, retro_tbel_2539, retro_tbel_2559, retro_tbel_2571, retro_tbel_2587, retro_tbel_270, retro_tbel_2713, retro_tbel_2716, retro_tbel_2752, retro_tbel_2809, retro_tbel_2835, retro_tbel_2854, retro_tbel_2926, retro_tbel_2993, retro_tbel_303, retro_tbel_3236, retro_tbel_3370, retro_tbel_3685, retro_tbel_3998, retro_tbel_4032, retro_tbel_4202, retro_tbel_4611, retro_tbel_4630, retro_tbel_484, retro_tbel_558, retro_tbel_687, retro_tbel_792, retro_tbel_793, retro_tbel_938,