RetrogeneDB ID: retro_chof_1227

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_231352:206..1064(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_chof_1227
AATGAAGAGGATTGGAGGAGAGCAGTGTGGGAGAAGAATACGAAGATGATCAAAATGCACAATCTGGAATACAGCCTGGG
GCAACGCAGCTTCAGGTTGGGAATGAATGCCTTTGGTGACAAGACCAATGATGAATTCAGGCAGCTTTCAAAACCAGGAA
CCCAAGAAGGAGGAAATGTGCTCTGAATCTCCCTCTGAAGTCCCCACATCTGTAGATTGGAGGGATAAAGGCTACGTGAC
TCCCGTGAAGGATCAGGATCACTGTGGTTCTTGTTGGGCTTTCAGTGCAACCAGTTCCCTGGAAGGACAGATGTTCCAGA
AAACTGGCATACCTGTTTCACTCAGTGAGCAGAAGCTGGTGGACTGTTCACAGGCTGAGGGCAATAGCAGCTGCAATGGC
GGCCTAATGGACAATGCCTTCCAGTATGTCCAGGACAACAAAGGCCTCGATTCAGAGGAATCCTATCCATATGTTGGAAA
GGACATGACCTGTAGCTACAAGCCTGAGTATTCTGCTGCCAACGACACTGGCTTCGTGGAGGTCACTCCACTGGAGAAGG
CCCTTATGGTGGCAGTGGCAACTGTAGGTCCCATCTTGGTTGTTATTGATACAAGCCATGATTCCTTCCAGTTCTATGAA
TCAGGGATTTATTATGAGCCAGACTGCAGCAGCAGAGACCTGGATCACGGGATCCTGGTGGTCGGCTATGGCTCTGAAGG
AACAGATTCAGATAACATTAAATACTGGCTCATCAAGGACAGCTGGGGTGAAAGTTGGGACATGGAGGGCTATGTAAAGA
TGGCCAGAGACCAGAACAACCACTGTGGAGTCACCACAAAGCCAGCTATCCCACCGTG

Alignment

ORF - retro_chof_1227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 92.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEEDWRRAVWEKNMKIIEVHNQEYSLGQHSFKLGMNAFGDMTSEEFRQV-MNGFQNKEHKKGEMFSESPS
          .EEDWRRAVWEKN.K.I..HN.EYSLGQ.SF.LGMNAFGD.T..EFRQ...N....KE....E..SE...
Retrocopy NEEDWRRAVWEKNTKMIKMHNLEYSLGQRSFRLGMNAFGDKTNDEFRQL>QNQEPKKEEMCSESPSE---

Parental  EVPTSVDWRDKGYVTPVKNQGHCGSCWAFSAAGSLEGQMFRKTGILVSLSEQNLVDCSRAEGNSGCNGGL
          .VPTSVDWRDKGYVTPVK.Q.HCGSCWAFSA..SLEGQMF.KTGI.VSLSEQ.LVDCS.AEGNS.CNGGL
Retrocopy -VPTSVDWRDKGYVTPVKDQDHCGSCWAFSATSSLEGQMFQKTGIPVSLSEQKLVDCSQAEGNSSCNGGL

Parental  MDNAFQYVQDNKGLDSEESYPYVGKDMNCSYKPEYSAANDTGFVEVAPLEKTLMAAVAAVGPISVAIDAS
          MDNAFQYVQDNKGLDSEESYPYVGKDM.CSYKPEYSAANDTGFVEV.PLEK.LM.AVA.VGPI.V.ID.S
Retrocopy MDNAFQYVQDNKGLDSEESYPYVGKDMTCSYKPEYSAANDTGFVEVTPLEKALMVAVATVGPILVVIDTS

Parental  HESFQFYESGIYYEPDCSSKDLDHGVLVVGYGFEETDSDNNKYWLVKNSWGESWGMEGYVKMARDRDNHC
          H.SFQFYESGIYYEPDCSS.DLDHG.LVVGYG.E.TDSDN.KYWL.K.SWGESW.MEGYVKMARD..NHC
Retrocopy HDSFQFYESGIYYEPDCSSRDLDHGILVVGYGSEGTDSDNIKYWLIKDSWGESWDMEGYVKMARDQNNHC

Parental  GIAT-KASYPTV
          G..T.KASYPTV
Retrocopy GVTT<KASYPTV

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_1227 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.

---

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,