RetrogeneDB ID: retro_pabe_2395

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:185605527..185606038(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC10
• Ensembl ID: ENSPPYG00000015776
• Aliases: None
• Description: zinc finger, CCHC domain containing 10 [Source:HGNC Symbol;Acc:25954]

Sequence

>retro_pabe_2395
ACTCCCATGGATCAGCTCATAGCCTGGAGACAAGCTGAAGCAAATAAGCAACATGTAAGATGTCAGAAATGCTTGGAATC
TGGACATTGGACTTATGAATGCACAGGAAAAAGAAAATACCTACACATGCCCTCAAGGACAGCAGAACTAGAGAAAGCTT
TAAAAGAAAACATATTATTATTACAACAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAAAAAAAAAGAAAAAAA
AAAAGGTCTAAGAGTGTAACCAGTTCCAGTAGCAGTAGCTGTGACAGTTCTGCAAGTGATTCTTCACCAGAGAGTGAAGA
AACATCTACCTCTTCCTCCTCAGAGGACAGTGACACTCATGACATTTACCTCTAGTTCCTCAGCCTCAGCCTCCTCCACA
ACCTCTTCCTCCTCCTCTGATTCAGACTCAGATTCCAGCTCTTCCAGTGGCAGCAGCACCAGCACAGATAGCAGCTCTGA
CGATGAACCACCAAAGAAGAAGAAAAAGAAA

Alignment

ORF - retro_pabe_2395 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.41 %
• Parental protein coverage: 98.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TPMHRLIARRQAEANKQHVRCQKCLEFGHWTYECTGKRKYLHRPSRTAELKKALKEKENRLLLQQSIGET
          TPM..LIA.RQAEANKQHVRCQKCLE.GHWTYECTGKRKYLH.PSRTAEL.KAL..KEN.LLLQQ.....
Retrocopy TPMDQLIAWRQAEANKQHVRCQKCLESGHWTYECTGKRKYLHMPSRTAELEKAL--KENILLLQQXXXXX

Parental  NVERKAKKKRSKSVTSSSSSSSDSS----ASDSSSESEETSTSSSSEDSDTDE-SSSSSSSSASSTTSSS
          ................S..SSS.SS....ASDSS.ESEETSTSSSSEDSDT.....SSSS.SASSTTSSS
Retrocopy XXXXXXXXXXXXXXSKSVTSSSSSSCDSSASDSSPESEETSTSSSSEDSDTHD>FTSSSSASASSTTSSS

Parental  SSDSDSDSSSSSSSSTSTESSSDDEPPKKKKKK
          SSDSDSDSSSSS.SSTST.SSSDDEPPKKKKKK
Retrocopy SSDSDSDSSSSSGSSTSTDSSSDDEPPKKKKKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.10 RPM
SRP007412_cerebellum	0.00 RPM	9.97 RPM
SRP007412_heart	0.00 RPM	5.00 RPM
SRP007412_kidney	0.00 RPM	4.08 RPM
SRP007412_liver	0.06 RPM	3.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2395 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2395 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2395 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001420	9 retrocopies	retro_chof_1243, retro_chof_1263, retro_chof_1773, retro_chof_2048, retro_chof_2132, retro_chof_2183, retro_chof_501, retro_chof_790, retro_chof_923,
Dasypus novemcinctus	ENSDNOG00000017302	1 retrocopy	retro_dnov_257,
Myotis lucifugus	ENSMLUG00000011366	4 retrocopies	retro_mluc_172, retro_mluc_2240, retro_mluc_2241, retro_mluc_2574,
Monodelphis domestica	ENSMODG00000013827	1 retrocopy	retro_mdom_1405,
Mus musculus	ENSMUSG00000018239	1 retrocopy	retro_mmus_269,
Pongo abelii	ENSPPYG00000015776	1 retrocopy	retro_pabe_2395 ,
Rattus norvegicus	ENSRNOG00000006943	3 retrocopies	retro_rnor_2037, retro_rnor_2528, retro_rnor_801,
Sorex araneus	ENSSARG00000007221	1 retrocopy	retro_sara_639,