RetrogeneDB ID: retro_chof_2462

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78053:4973..5587(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMZ2
• Ensembl ID: ENSCHOG00000000493
• Aliases: None
• Description: archaelysin family metallopeptidase 2 [Source:HGNC Symbol;Acc:28041]

Sequence

>retro_chof_2462
GATATCCTGAAGTTCTTAAAAAAAGAAGAAACTTCAAAATGCCTTCTCTGTTATAGGGATAACAATGACTGATCTTTACC
CAAGAGACTCCTGGAATTTTGTCACTGACAAGCCTCCTTGATAGATGGCATGGGAATCATTCAGCTTTCCCAAGTATGGC
AGTGATTTTTACAGCTCATGCTATGAAGGCAAAGTGAAGCAGCTCTGGAAAACATCTCCAAATAACTATTTATCTTTGAA
AACTATCATATTCCTGAAATAGCTAGTACTTTGCTACTTTGATCCTTTAAGACCTTAACCCATGAGACTAGACATAGATG
TGAACTGCGACACTGCCAGTAGCTCTCATGCCTAATGCAAGGATTCAACTGCATGGAAGAAGCTAACCAGTGCTCTCTTT
GCCCCATCTGATTATGCAAGTTGCAGGGTATTATTTATGGCATGATCATAGAAAGATACAAAATGCTAGTAAGGTGGATT
CATGAAAAATCTGCTGTCATACCAGGTATAACTATAAAACACAGTCTTGAGAATAACATGCATTACCACAGTCCTTGGAA
GCCTTTAGAGAATGGAAAGTGTGGATAATAAAATGCCTTGCTGTTCTCCAAAAA

Alignment

ORF - retro_chof_2462 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.15 %
• Parental protein coverage: 57.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DILKFLKK-KKPRNAFCVVGITMIDLYPRDSWNFVFG-QASLTDGVGI-FSFARYGSDFYSANYKGKVKK
          DILKFLKK.KK..NAF.V.GITM.DLYPRDSWNFV...QASL.DG.GI.FSF..YGSDFYS..Y.GKVK.
Retrocopy DILKFLKK>KKLQNAFSVIGITMTDLYPRDSWNFVTD<QASLIDGMGI>FSFPKYGSDFYSSCYEGKVKQ

Parental  LQKTSSSDY-SVFDNYYIPEITSILLLRSCKTLSHELGHIFGLRHCQWLSCLMQGSNHLEEADRRPLNLC
          L.KTS...Y...F.NY.IPEI.S.LLL.S.KTL.HE..H...LRHCQ.LSCLMQG.N..EEA......LC
Retrocopy LWKTSPNNY<FIFENYHIPEIASTLLL*SFKTLTHETRHRCELRHCQ*LSCLMQGFNCMEEANQ--CSLC

Parental  PICLRKLQCALGFSIVERYKALVRWMDDESADIPGESPEHSREDNVH-LPKPVEAFKEWREWIIKCLAVL
          PI.L.KLQ......I.ERYK.LVRW....SA.IPG....HS.E.N.H.LP...EAF.EW..WIIKCLAVL
Retrocopy PI*LCKLQGIIYGMIIERYKMLVRWIHEKSAVIPGITIKHSLENNMH<LPQSLEAFREWKVWIIKCLAVL

Parental  QK
          QK
Retrocopy QK

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_2462 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009345	1 retrocopy	retro_btau_429,
Choloepus hoffmanni	ENSCHOG00000000493	1 retrocopy	retro_chof_2462 ,
Callithrix jacchus	ENSCJAG00000000254	1 retrocopy	retro_cjac_2798,
Cavia porcellus	ENSCPOG00000013061	1 retrocopy	retro_cpor_1226,
Equus caballus	ENSECAG00000011450	2 retrocopies	retro_ecab_440, retro_ecab_864,
Felis catus	ENSFCAG00000019195	1 retrocopy	retro_fcat_760,
Myotis lucifugus	ENSMLUG00000006771	2 retrocopies	retro_mluc_1540, retro_mluc_2056,
Mustela putorius furo	ENSMPUG00000014570	1 retrocopy	retro_mputfur_1224,
Pteropus vampyrus	ENSPVAG00000017239	2 retrocopies	retro_pvam_1453, retro_pvam_989,