RetrogeneDB ID: retro_pabe_1676

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:43766065..43766526(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND5
• Ensembl ID: ENSPPYG00000019290
• Aliases: None
• Description: zinc finger, AN1-type domain 5 [Source:HGNC Symbol;Acc:13008]

Sequence

>retro_pabe_1676
CCAACCTCAGATTCTGCATCTGTACAGAGAGCAGACACTAGCTTAAACAACTGTGAAGGTGCTGCTGGCAGCACATCTGA
AAAATCAAGAAATGTGACTGTGGCTGCCTTGCCTGTAACTCAGCAAATGACAGAAATGAGCATTTCAACAGAGGACAAAA
TACCCCAAAAACAGAGATGTCAGAGCCAGTTGTCACTCAGCCCAGTCCATCAGTTTCTCAGCCCAGTACTTCTCAGAGTG
AAGAAAAAGCTCCTGAATTGCCCAAACCAAAGAAAAACAGATGTTTCATGTGCAGAAAGAAAGTTGGTCTTACAGGGTTT
GACTGCCGATGTGGAAATTTGTTTTGTGGACTTCACTGTTACTCTGACAAGCACAACTGTCCGTATGATTACAAAGCAGA
AGCTGCAGCAAAAATCAGAAAAGAGAATCCAGTTGTTGTGGCTGAAAAAATTCAGAGAATA

Alignment

ORF - retro_pabe_1676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 72.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PTSDSASVQRADTSLNNCEGAAGSTSEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPS
          PTSDSASVQRADTSLNNCEGAAGSTSEKSRNV.VAALPVTQQMTEMSIS.EDKI...K..........P.
Retrocopy PTSDSASVQRADTSLNNCEGAAGSTSEKSRNVTVAALPVTQQMTEMSISTEDKI-PQKQRCQSQLSLSPV

Parental  PSVSQPSTSQSEEKAPELP-KPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYKAEAAAK
          .....P.......K....P.KPKKNRCFMCRKKVGLTGFDCRCGNLFCGLH.YSDKHNCPYDYKAEAAAK
Retrocopy HQFLSPVLLRVKKKLLNCP<KPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHCYSDKHNCPYDYKAEAAAK

Parental  IRKENPVVVAEKIQRI
          IRKENPVVVAEKIQRI
Retrocopy IRKENPVVVAEKIQRI

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	15.09 RPM	14.54 RPM
SRP007412_cerebellum	17.63 RPM	17.27 RPM
SRP007412_heart	8.67 RPM	9.60 RPM
SRP007412_kidney	14.88 RPM	17.47 RPM
SRP007412_liver	17.87 RPM	21.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1676 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1676 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2063
Pan troglodytes	retro_ptro_1375
Gorilla gorilla	retro_ggor_1485

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002366	2 retrocopies	retro_chof_1050, retro_chof_1846,
Cavia porcellus	ENSCPOG00000005076	2 retrocopies	retro_cpor_1398, retro_cpor_774,
Felis catus	ENSFCAG00000027317	1 retrocopy	retro_fcat_641,
Homo sapiens	ENSG00000107372	1 retrocopy	retro_hsap_2063,
Gorilla gorilla	ENSGGOG00000008957	1 retrocopy	retro_ggor_1485,
Myotis lucifugus	ENSMLUG00000007173	2 retrocopies	retro_mluc_1233, retro_mluc_1993,
Monodelphis domestica	ENSMODG00000004426	1 retrocopy	retro_mdom_1910,
Mustela putorius furo	ENSMPUG00000008951	1 retrocopy	retro_mputfur_143,
Mus musculus	ENSMUSG00000024750	1 retrocopy	retro_mmus_1176,
Oryctolagus cuniculus	ENSOCUG00000000795	1 retrocopy	retro_ocun_1546,
Procavia capensis	ENSPCAG00000007436	1 retrocopy	retro_pcap_112,
Pongo abelii	ENSPPYG00000019290	1 retrocopy	retro_pabe_1676 ,
Vicugna pacos	ENSVPAG00000000700	1 retrocopy	retro_vpac_23,