RetrogeneDB ID: retro_chof_1817

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_39213:5145..5642(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MXI1
• Ensembl ID: ENSCHOG00000006556
• Aliases: None
• Description: MAX interactor 1, dimerization protein [Source:HGNC Symbol;Acc:7534]

Sequence

>retro_chof_1817
AACAGCAGGAGCAGCAACACCGGCACTACCAACAGGTCTACAAACGAGGAGCTAGAAAAGAATCAACCAGCCCATCTGCA
CCCAGAATACTTACAGGTTCTCATTCCACTAGGGCGAGATTGCACCAGGCACGCAACAACTTGGTTTACTCAACAAAGCG
AAAGCACATATCAAGAAGCTTGAAGAAGCTGAAAGGAAGAGCCAGCACCAGCTTGAGAACTTTGAATGAGGACAGAGATT
TTTAAAGGGGTAATTGGAAAAGCTGCAGGGTCCTCAGGAGACAGAACAAATAAGAATGGACAGTACCGGATCAACTATTT
CTTTAGATCATTCTGATTCCAAGAGAGAAGAAATTGATGTGGGTGTTGAAAGAGTTCTCCCATGGAGAAATGGACAATAT
CACCAGCATCAGTGACACTGAAGACCATAGCAGCCTGCAGGGCATTAGGAGTAAGGAGGGTTACTCGAGGACCAGTGTCA
CACTTCCATTCACTTCT

Alignment

ORF - retro_chof_1817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.52 %
• Parental protein coverage: 86.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NNGSSNTTPANKSTHNELEKNRRAHLRLCLERLKVLIPLGPDCTRHTT-LGLLNKAKAHIKKLEEVERKS
          N..SSNT...N.ST..ELEKN..AHL....E.L.VLIPLG.DCTRH.T.LGLLNKAKAHIKKLEE.ERKS
Retrocopy NSRSSNTGTTNRSTNEELEKNQPAHLHP--EYLQVLIPLGRDCTRHAT>LGLLNKAKAHIKKLEEAERKS

Parental  QHQLENLEREQRFLKRRLEQLQGPQEMERIRMDSIGSTISSDRSDSEREEIEVDVEST-EFSHGEVDNIS
          QHQLEN.E..QRFLK..LE.LQGPQE.E.IRMDS.GSTIS.D.SDS.RE..E.DV....EFSHGE.DNI.
Retrocopy QHQLENFE*GQRFLKG*LEKLQGPQETEQIRMDSTGSTISLDHSDSKRE--EIDVGVE>EFSHGEMDNI-

Parental  TTSISDIDDHSSLQSIGSDEGYSSASVKLSFTS
          .TSISD..DHSSLQ.I.S.EGYS..SV.L.FTS
Retrocopy -TSISDTEDHSSLQGIRSKEGYSRTSVTLPFTS

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_1817 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003047	1 retrocopy	retro_chof_1224,
Choloepus hoffmanni	ENSCHOG00000006556	2 retrocopies	retro_chof_1350, retro_chof_1817 ,
Cavia porcellus	ENSCPOG00000022901	1 retrocopy	retro_cpor_574,
Dasypus novemcinctus	ENSDNOG00000002479	2 retrocopies	retro_dnov_1336, retro_dnov_668,
Mus musculus	ENSMUSG00000025025	1 retrocopy	retro_mmus_1948,
Sus scrofa	ENSSSCG00000022128	1 retrocopy	retro_sscr_947,
Vicugna pacos	ENSVPAG00000003400	2 retrocopies	retro_vpac_483, retro_vpac_595,