RetrogeneDB ID: retro_chof_383

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_102102:254..1127(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000001365
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007548
• Aliases: None
• Description: None

Sequence

>retro_chof_383
TCAAATGAAGAGGGTTGGAGGAGAGCAGTGTAAGAGAAGAATATGAAAGTGATCGAACTGCACAATCTAGAATACGGCCT
GGGGCAACACAGCTTCAAGATGGGAATGAATGCCTTTAGTGACATGACCAATGAAGAATTCAGGCAGGTGATGAATGGCT
TTTAAAACCAGCAACACCAGAAGGGGAAAATATTCTATGAACTTCCCTCTGATGTCCCCAAATCTGTGAATTGGCATAAG
AAAGGCCACGTGACTCCCATGAAGAATCAGGGTCAGTGTGGTTCTTGTTGGGCTTTCAGTGCACCTGGTTGCCTGGAAGG
ACAGATGTTCCAGAAAGCTGGCGAACTTGTTTTACTCAGGGAGTATAACCTGCTGTACTGCTCTCAGGCTGAGGGCGATA
ACGGCTACAATGGTGTCCTAATGGACAATGCTTTCCAGTATGTTCAGGACAACAAAGGCCTCAATTCAGAGAAATCCTAT
CCTTTATTGAAAAGGACATGACCTGTCGCTACAAGCCCAAGAATTCTGCTGCCAATGACACTGGCTTCGTGGACATCCCT
CTGCAGGAGAAAGCACTTAATGAAGGCATTGGCAACTATGGGTCCCATCTTGGTTGCTATTGATGCAAACCATGTCTCCT
TCCAGTTCTACTCATCAGTCATTTATTATGAGTCAGACTACAGTGGCAGAGACCTGGATGACAGTGTCCTGGTGGTTGTC
TATAGCTTTGAAGGAACAGATTGAAATAACAATAAATAGTGGCTTGTCAAGAACAGCTGGGTTGAAGATCAGGGCATGGA
GGGCTACATAAAGATAGTCAGAGACCAGAATAACCACTGTGAAGTAACCACATCAACCAACTATCCCACCATG

Alignment

ORF - retro_chof_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.92 %
• Parental protein coverage: 92.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSEEDWRRAVWEKNMKIIEVHNQEYSLGQHSFKLGMNAFGDMTSEEFRQVMNGFQNKEHKKGEMFSESPS
          S.EE.WRRAV.EKNMK.IE.HN.EY.LGQHSFK.GMNAF.DMT.EEFRQVMNGF.N..H.KG..F.E.PS
Retrocopy SNEEGWRRAV*EKNMKVIELHNLEYGLGQHSFKMGMNAFSDMTNEEFRQVMNGF*NQQHQKGKIFYELPS

Parental  EVPTSVDWRDKGYVTPVKNQGHCGSCWAFSAAGSLEGQMFRKTGILVSLSEQNLVDCSRAEGNSGCNGGL
          .VP.SV.W..KG.VTP.KNQG.CGSCWAFSA.G.LEGQMF.K.G.LV.L.E.NL..CS.AEG..G.NG.L
Retrocopy DVPKSVNWHKKGHVTPMKNQGQCGSCWAFSAPGCLEGQMFQKAGELVLLREYNLLYCSQAEGDNGYNGVL

Parental  MDNAFQYVQDNKGLDSEESYP-YVGKDMNCSYKPEYSAANDTGFVEVAPLEKT-LMAAVAAVGPISVAID
          MDNAFQYVQDNKGL.SE.SYP....KDM.C.YKP..SAANDTGFV.....EK..LM.A.A..GPI.VAID
Retrocopy MDNAFQYVQDNKGLNSEKSYP<FIEKDMTCRYKPKNSAANDTGFVDIPLQEKA>LMKALATMGPILVAID

Parental  ASHESFQFYESGIYYEPDCSSKDLDHGVLVVGYGFEETDSDNNKYWLVKNSWGESWGMEGYVKMARDRDN
          A.H.SFQFY.S.IYYE.D.S..DLD..VLVV.Y.FE.TD..NNK.WLVKNSW.E..GMEGY.K..RD..N
Retrocopy ANHVSFQFYSSVIYYESDYSGRDLDDSVLVVVYSFEGTD*NNNK*WLVKNSWVEDQGMEGYIKIVRDQNN

Parental  HCGIATKASYPTV
          HC...T...YPT.
Retrocopy HCEVTTSTNYPTM

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_383 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007548	8 retrocopies	retro_chof_1227, retro_chof_1332, retro_chof_1345, retro_chof_141, retro_chof_1464, retro_chof_2392, retro_chof_383 , retro_chof_424,
Dasypus novemcinctus	ENSDNOG00000012037	1 retrocopy	retro_dnov_2387,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Otolemur garnettii	ENSOGAG00000001349	2 retrocopies	retro_ogar_1053, retro_ogar_1373,
Ochotona princeps	ENSOPRG00000001030	2 retrocopies	retro_opri_186, retro_opri_499,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tupaia belangeri	ENSTBEG00000016406	1 retrocopy	retro_tbel_2841,