RetrogeneDB ID: retro_chof_1231

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_232189:3451..4006(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPHLN1
• Ensembl ID: ENSCHOG00000010693
• Aliases: None
• Description: periphilin 1 [Source:HGNC Symbol;Acc:19369]

Sequence

>retro_chof_1231
AGCAGATCTGGCTCCAGTGTCAACAGTAAAAGCTACTTTCTGGAAAAAAGCAAAATGTACTGTTTCCATGAATCTCAACA
TAGAAAGTCCATGCGTGCTGGTGCATCCTACAAATAGCAGAATGAAGGAAAGCCAGAAAGAGGTAAAGAGAGACCTGTCC
AGTCTTTGAAAACATTAACAGACACTTCACCCTCAAGTTCTTCAGCAGTTATTTCATCAAAGGTGTTAGACAAGCCCAGT
AGGCCCACTGAAAAGGAACTTGCTGAGGCTGCAAGCAAGTGGGCTGCTGAAAAGCTAGAGAAGGCAGATGATAGCAACTT
ACCTGACATTTCTGAGTATGAGGCAGGATCCACAGCACCACTGTTTATTGACCAGCCAGAAGGACCTGAGTCGAATGAAA
CAGATGACATAGAATTATTTAAAGACAGTCAGCTAACCAGTCACTCTAAAGCAATAGCATCAAAACCCAAAGAGATTGAA
CAGGTTTATCGACAGACTGTGAAACTTTCGGGATGGGTTGTGAAAATGCTGATTGAAAAAGATCTTTCATTAGAC

Alignment

ORF - retro_chof_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 54.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRSGSSVSSRSYSPERSKTYSFHQSQHRKSVRSGASYKRQKEGKPARGKERPVQSLKTSRDTSPSSSSAV
          SRSGSSV.S.SY..E.SK.Y.FH.SQHRKS.R.GASYK.Q.EGKP.RGKERPVQSLKT..DTSPSSSSAV
Retrocopy SRSGSSVNSKSYFLEKSKMYCFHESQHRKSMRAGASYK*QNEGKPERGKERPVQSLKTLTDTSPSSSSAV

Parental  ASSK-LDKHSRITEKDLAEAASKWAAEKLEKADDSNLPEISEYEAGSTAPLFIDQPEEPESNATDGIELF
          .SSK.LDK.SR.TEK.LAEAASKWAAEKLEKADDSNLP.ISEYEAGSTAPLFIDQPE.PESN.TD.IELF
Retrocopy ISSKVLDKPSRPTEKELAEAASKWAAEKLEKADDSNLPDISEYEAGSTAPLFIDQPEGPESNETDDIELF

Parental  EDSQLNSRSKAIASKTKEIEQVYRQ-DCETFGM-VVKMLIEKDPSLE
          .DSQL.S.SKAIASK.KEIEQVYRQ.DCETFGM.VVKMLIEKD.SL.
Retrocopy KDSQLTSHSKAIASKPKEIEQVYRQ<DCETFGM>VVKMLIEKDLSLD

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_1231 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010693	1 retrocopy	retro_chof_1231 ,
Callithrix jacchus	ENSCJAG00000017726	1 retrocopy	retro_cjac_1547,
Cavia porcellus	ENSCPOG00000012266	2 retrocopies	retro_cpor_744, retro_cpor_745,
Dasypus novemcinctus	ENSDNOG00000002007	1 retrocopy	retro_dnov_1790,
Equus caballus	ENSECAG00000016067	1 retrocopy	retro_ecab_209,
Mus musculus	ENSMUSG00000036167	3 retrocopies	retro_mmus_1657, retro_mmus_3561, retro_mmus_79,
Otolemur garnettii	ENSOGAG00000004012	2 retrocopies	retro_ogar_1387, retro_ogar_2103,
Tarsius syrichta	ENSTSYG00000010740	1 retrocopy	retro_tsyr_2044,