RetrogeneDB ID: retro_pabe_1235

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:37586312..37587125(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM92A1
• Ensembl ID: ENSPPYG00000018744
• Aliases: None
• Description: family with sequence similarity 92, member A1 [Source:HGNC Symbol;Acc:30452]

Sequence

>retro_pabe_1235
GGCCCCTGCAAGGTCCCCTGCTGTGCGCGAGGCAGCATGATGAGGCGCACCCTGGAAAACCGGAACGCTCAAACGAAACA
ACTGCAAACAGCTGTCTCAAACGTGGAGAAGCATTTTGGAGAACTGTGCCAAATCTTCGCTGCCTATGTGCGGAAAACTG
CCTGGCTGAGAGACAAAGCAGACCTCCTGGTGAATGAAATCAACGCGTATGCTGCTACAGAGACCCCACATTTAAAGCTG
GGCCTGATGAACTTTGCTGATGAGTTTGCCAAACTTCAGGATTATCGACAAGCAGAGGTTGAAAGACTTGAAGCCAAAGT
AGTTGAACCCTTGAAAGCTTATGGGACCATTGTGAAAATGAAACGGGATGACCTCAAAGCAACATTCACAGCAAGGAATC
GAGAAGCTAAGCAATTAACGCAATTAGAAAGAACACGTCAGCGAAACCCATCTGATTGACATGTTATTTCACAGGCAGAA
ACGGAATTGCAGAGAACTGCAATGGATGCTACCCGAACAAGCCGTCATCTGGAGGAAACTATTAACAACTTTGAAAGGCA
GAAAATGAAGGATATAAAGACTATATTTTCTGAATTTATCACAATCGAAATGTTATTTCACGGCAAAGCTTTAGAGGTCT
ACGCTGCTGCCTACCGGAATATACAAAACATTGATGAAGATGAAGATTTAGAGGTTTTCCGAAATTCTCTGTATGCACCA
GATTATTCATCTCGTTTAGATATTGTAAGAGCAAATTCAAAGTCACCTCTTCAGAGATCACTGTCAGCTAAGTGTGTATC
TGGAACAGAACAG

Alignment

ORF - retro_pabe_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 88.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPRKVPGRARGSAMRRTLENRNAQTKQLQTAVSNVEKHFGELCQIFAAYVRKTARLRDKADLLVNEINAY
          GP.KVP..ARGS.MRRTLENRNAQTKQLQTAVSNVEKHFGELCQIFAAYVRKTA.LRDKADLLVNEINAY
Retrocopy GPCKVPCCARGSMMRRTLENRNAQTKQLQTAVSNVEKHFGELCQIFAAYVRKTAWLRDKADLLVNEINAY

Parental  AATETPHLKLGLMNFADEFAKLQDYRQAEVERLEAKVVEPLKTYGTIVKMKRDDLKATLTARNREAKQLT
          AATETPHLKLGLMNFADEFAKLQDYRQAEVERLEAKVVEPLK.YGTIVKMKRDDLKAT.TARNREAKQLT
Retrocopy AATETPHLKLGLMNFADEFAKLQDYRQAEVERLEAKVVEPLKAYGTIVKMKRDDLKATFTARNREAKQLT

Parental  QLERTRQRNPSDRHVIVSAETELQRAAMDASRTSRHLEETINNFERQKMKDIKTIFSEFITIEMLFHGKA
          QLERTRQRNPSD.HVI..AETELQR.AMDA.RTSRHLEETINNFERQKMKDIKTIFSEFITIEMLFHGKA
Retrocopy QLERTRQRNPSD*HVISQAETELQRTAMDATRTSRHLEETINNFERQKMKDIKTIFSEFITIEMLFHGKA

Parental  LEVYTAAYQNIQNIDEDEDLEVFRNSLYAPDYSSRLDIVRANSKSPLQRSLSAKCVSGTGQ
          LEVY.AAY.NIQNIDEDEDLEVFRNSLYAPDYSSRLDIVRANSKSPLQRSLSAKCVSGT.Q
Retrocopy LEVYAAAYRNIQNIDEDEDLEVFRNSLYAPDYSSRLDIVRANSKSPLQRSLSAKCVSGTEQ

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	0.44 RPM	7.85 RPM
SRP007412_cerebellum	0.36 RPM	8.39 RPM
SRP007412_heart	0.27 RPM	3.64 RPM
SRP007412_kidney	0.20 RPM	3.88 RPM
SRP007412_liver	0.09 RPM	3.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1235 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009105	1 retrocopy	retro_cfam_1072,
Echinops telfairi	ENSETEG00000013003	1 retrocopy	retro_etel_522,
Homo sapiens	ENSG00000188343	1 retrocopy	retro_hsap_1485,
Gorilla gorilla	ENSGGOG00000006452	1 retrocopy	retro_ggor_1137,
Loxodonta africana	ENSLAFG00000003954	1 retrocopy	retro_lafr_201,
Microcebus murinus	ENSMICG00000006797	1 retrocopy	retro_mmur_415,
Monodelphis domestica	ENSMODG00000007447	2 retrocopies	retro_mdom_1239, retro_mdom_827,
Mustela putorius furo	ENSMPUG00000009112	1 retrocopy	retro_mputfur_1183,
Nomascus leucogenys	ENSNLEG00000002773	1 retrocopy	retro_nleu_1707,
Otolemur garnettii	ENSOGAG00000002972	1 retrocopy	retro_ogar_654,
Oreochromis niloticus	ENSONIG00000002446	1 retrocopy	retro_onil_57,
Procavia capensis	ENSPCAG00000011171	1 retrocopy	retro_pcap_272,
Pongo abelii	ENSPPYG00000018744	2 retrocopies	retro_pabe_1235 , retro_pabe_2497,
Tarsius syrichta	ENSTSYG00000012502	1 retrocopy	retro_tsyr_975,
Tursiops truncatus	ENSTTRG00000012378	1 retrocopy	retro_ttru_45,