RetrogeneDB ID: retro_chof_1106

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_201295:3176..3990(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDH1A2
• Ensembl ID: ENSCHOG00000006418
• Aliases: None
• Description: aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:15472]

Sequence

>retro_chof_1106
GCCATTGCTTCCCACAAAGATGTGGACAAAGTGGCATTCACAAATTCCACCAAGGTTGGTCACTTCATCTAGATTGCTGT
GGAGAGCAGCAACCCCAAGAGATTGACCCTGGAGCTGGGGGAAAAGAGCCTCAACACCATCATGTCGGGTGCTGATGTGG
ACTGGGTTGTTGAGCAGGCCCACTTACCCTGTTCTTCAACCAGGGCCTGTGCTGCTGTGCCATCTCCTGGACCTTTGTGC
AAGAAGACATCTAACCTGAGTTGATAGAGCTGAATGTCATCTGGGCCAGGTCTTGGGTTGTTAGAAACCCTTTTGTCCGA
TCAAGCAGGGTCAGGTGGATGAAACGCAGTTTAATGAGATCCATGACTATATCAAATCTGGGAAGCAAGAAGGGAGAAGC
TATTGTGTGGTGATTGTGGTGGAGCTGCTGCTGACCATGGCTGCTTCATTCAGTCCACTGTGTTTAGAGATGAGTAAGAT
TTCATGACCATTGCAAAGGAGGAGATCTTTGGGTCAATGAAGTGGATCCTGAAGTTTGAGACCATAGAGGAAGTCATATG
GAGAACAAAAATTCCAAATATGGGCTTTGGCTGCAGCTGTTTTCACAAAGAACATGTACAAGGCCAGTTACCTGTCCCTG
CCCCTCCAGACTAGCACTGTGTGGGTCAACTGCTATGAAGTGTTTGGGGCCCAGTCACCTTTCTGTGGCTACAAGATGTC
TGGTAATGGCCAAGAGCTCAGTGAATACAGTCTGCAAGGGTATACTCAAGTGAAAACAGTCACAATTATAATCAAAGTTC
CTCATAAGAACTCA

Alignment

ORF - retro_chof_1106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.36 %
• Parental protein coverage: 68.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AIASHVGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQG-VFFNQG
          AIASH...DK.AFT.ST.VG..I..A...SN.KR.TLELG.KS.N.I...AD.D..VEQAH....FFNQG
Retrocopy AIASHKDVDKVAFTNSTKVGHFI*IAVESSNPKRLTLELGEKSLNTIMSGADVDWVVEQAHLP<LFFNQG

Parental  QCCTAGSRIFVEESIYEEFVRRSVERAKRRIVGSP-FDPTTEQGPQIDKKQYNKILELIQSGVAEGA-KL
          .CC.A.S..FV.E.I..E.....V..A....V..P.F.P...QG.Q.D..Q.N.I...I.SG..EG..KL
Retrocopy LCCCAISWTFVQEDI*PELIELNVIWARSWVVRNP<FCPI-KQG-QVDETQFNEIHDYIKSGKQEGR<KL

Parental  ECG--GKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFG-LVAAVFTN
          .CG..G......G.FI..TVF....D.M.IAKEEIFG....IL.F.T..EVI.R......G.L.AAVFT.
Retrocopy LCGDCGGAAADHGCFIQSTVFRDE*DFMTIAKEEIFGSMKWILKFETIEEVIWRTKIPNMG>LAAAVFTK

Parental  DINKALTVSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGEFGLREYSEIKTVT--VKIPQKNS
          ...KA...S...Q..TVW.NCY....AQSPF.G.KMSGNG.E..E..L..Y...KTVT...K.P.KNS
Retrocopy NMYKASYLSLPLQTSTVWVNCYEVFGAQSPFCGYKMSGNGQELSEYSLQGYTQVKTVTIIIKVPHKNS

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_1106 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002143	1 retrocopy	retro_chof_869,
Choloepus hoffmanni	ENSCHOG00000002670	1 retrocopy	retro_chof_2670,
Choloepus hoffmanni	ENSCHOG00000006418	1 retrocopy	retro_chof_1106 ,
Erinaceus europaeus	ENSEEUG00000012262	1 retrocopy	retro_eeur_15,
Monodelphis domestica	ENSMODG00000008641	1 retrocopy	retro_mdom_254,
Pan troglodytes	ENSPTRG00000007113	1 retrocopy	retro_ptro_118,
Sorex araneus	ENSSARG00000012720	1 retrocopy	retro_sara_40,
Sarcophilus harrisii	ENSSHAG00000012217	1 retrocopy	retro_shar_111,
Tarsius syrichta	ENSTSYG00000004549	1 retrocopy	retro_tsyr_8,
Tursiops truncatus	ENSTTRG00000002361	1 retrocopy	retro_ttru_932,