RetrogeneDB ID: retro_chof_1919

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_422764:1..741(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIDA
• Ensembl ID: ENSCHOG00000010095
• Aliases: None
• Description: axin interactor, dorsalization associated [Source:HGNC Symbol;Acc:25761]

Sequence

>retro_chof_1919
TTAGCAAGACATCTACAGAAAGAGGCCCGAGTTCATAATAATTCCGAATTCACAGAAGAAGAAAAGAAAACAATAGCAGA
ATTGCAACATTTCTTGGAATTTCAGCTTTATAGTCCACACAGTTCCAAGAAGAAACTGGAGGATGTGAAGAAGATAGAAC
CAATCCTAAAGAATATTCTTACATATAATAAAGAATTCCCATTTGATGTTCAGCCTGTCCCATTAAGAATTTTAGCAGCT
GGTGAAGAAGAAAATTTGGAATTTGAAGATGATGAAGAAGAGGGTGGTGCTGGAGCTGGGTCTACTGATCCCTTTCCTGC
TAGAGTTCCCAGTACTTTATTACCAAGGTTGCCCTCAGAACCGGGAATGACATTACTCACTATCAGGATTGAGAAGATTG
GTCTGAAAGATGCTGGGCAGTGCATCGATCCCTATATTATAGTTAGTGTAAAAGATCTGAATGGCATAGATTTAACTTCT
GTGCAAGATATTCCTGTGATTGAAAAAAAGAAGACACATATGTTCATTTTAATGTGGACATTGAGCTCCAGAAGCATGTT
GAAAAATTAACCAAAGGTGCAGCTATCTTCTTTGAATTCAAACACTACAAGCCTAAGAAAAGATTTACCAGCACCAAGTG
TTTTGCTTTCATGGAGATGGATGAAATTAAACCTGGGCCAATTGTAATAGAACTATACAAGAAACCCACTGACTTTAAAA
GAAAGAAATTGCAGTTATTG

Alignment

ORF - retro_chof_1919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.43 %
• Parental protein coverage: 94.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LARHLQKEAQAQHNNSEFTEEQKKTIGKIATCLELRSAALQSTQSQEEFKLEDLKKLEPILKNILTYNKE
          LARHLQKEA...HNNSEFTEE.KKTI......LE.....L.S..S....KLED.KK.EPILKNILTYNKE
Retrocopy LARHLQKEARV-HNNSEFTEEEKKTIAELQHFLEFQ---LYSPHSSKK-KLEDVKKIEPILKNILTYNKE

Parental  FPFDVQPVPLRRILAPGEEENLEFEEDEEEGGAGAGSPDFFPARVPGTLLPRLPSEPGMTLLTIRIEKIG
          FPFDVQPVPLR.ILA.GEEENLEFE.DEEEGGAGAGS.D.FPARVP.TLLPRLPSEPGMTLLTIRIEKIG
Retrocopy FPFDVQPVPLR-ILAAGEEENLEFEDDEEEGGAGAGSTDPFPARVPSTLLPRLPSEPGMTLLTIRIEKIG

Parental  LKDAGQCIDPYITVSVKDLNGIDLTPVQDTPVAS-RKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHY
          LKDAGQCIDPYI.VSVKDLNGIDLT.VQD.PV....KEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHY
Retrocopy LKDAGQCIDPYIIVSVKDLNGIDLTSVQDIPVIE<KKEDTYVHFNVDIELQKHVEKLTKGAAIFFEFKHY

Parental  KPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLL
          KPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLL
Retrocopy KPKKRFTSTKCFAFMEMDEIKPGPIVIELYKKPTDFKRKKLQLL

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_1919 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007593	2 retrocopies	retro_btau_1163, retro_btau_573,
Choloepus hoffmanni	ENSCHOG00000010095	2 retrocopies	retro_chof_1919 , retro_chof_97,
Dasypus novemcinctus	ENSDNOG00000008380	5 retrocopies	retro_dnov_1765, retro_dnov_1909, retro_dnov_1961, retro_dnov_2172, retro_dnov_2280,
Homo sapiens	ENSG00000186063	4 retrocopies	retro_hsap_1901, retro_hsap_2076, retro_hsap_2998, retro_hsap_410,
Gorilla gorilla	ENSGGOG00000015289	3 retrocopies	retro_ggor_1394, retro_ggor_1627, retro_ggor_2077,
Macaca mulatta	ENSMMUG00000015025	1 retrocopy	retro_mmul_1918,
Monodelphis domestica	ENSMODG00000004774	3 retrocopies	retro_mdom_1417, retro_mdom_1418, retro_mdom_1448,
Nomascus leucogenys	ENSNLEG00000013583	1 retrocopy	retro_nleu_748,
Oryctolagus cuniculus	ENSOCUG00000017030	1 retrocopy	retro_ocun_688,
Pongo abelii	ENSPPYG00000000196	2 retrocopies	retro_pabe_2015, retro_pabe_2485,
Pan troglodytes	ENSPTRG00000002010	3 retrocopies	retro_ptro_1254, retro_ptro_1528, retro_ptro_2027,
Tarsius syrichta	ENSTSYG00000005745	3 retrocopies	retro_tsyr_101, retro_tsyr_1795, retro_tsyr_514,
Tursiops truncatus	ENSTTRG00000016594	1 retrocopy	retro_ttru_1084,