RetrogeneDB ID: retro_pabe_118

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:14290772..14291825(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000012782
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM185A
• Ensembl ID: ENSPPYG00000020809
• Aliases: TMEM185A, FAM11A
• Description: transmembrane protein 185A [Source:RefSeq peptide;Acc:NP_001126120]

Sequence

>retro_pabe_118
ATGAACCCCAGGGGCCTGTTCCAGGACTTCAACCCCAGTAAGTTTCTCATCTATACCTGCCTGCTGCTCTTCTCGGTGCT
GCTGCCCCTCCGCCTGGACGGCATCATCCAATGGAGCTACTGGGCCGTCTTTGCCCCCATATGGCTGTGGAAGCTTCTAG
TCGTCGCAGGCGCCTCCGTGGGCGCGGGCGTTTGGGCCCGCAACCCTCGCTACCGCACCGAGGGAGAGGCCTGTGTGGAG
TTCAAAGCCATGCTGATCGCTGTGGTCATCCACCTGCTGCTGCTCATGTTCGAAGTCCTGGTCTGCGACAGGGTGGAGAG
GGGCACCCACTTCTGGCTGCTGGTCTTCATGCCTCTCTTCTTCGTGTCCCCCGTGTCCGTGGCTGCCTGCGTCTGGGGCT
TTCGACACGATAGGTCGCTGGAGCTGGAGATCCTGTGCTCGGTCAACATACTGCAGTTCATCTTCATCGCCCTAAAGCTG
GACAGGATTATTCACTGGCCGTGGCTAGTGGTGTTTGTGCCCCTGTGGATCCTCATGTCGTTCCTTTGCCTGGTCGTTCT
CTATTACATCGTCTGGTCCCTCCTGTTCCTGCGGTCCCTGGATGTGGTTGCCGAGCAGCGAAGAACACACGTGACCATGG
CTATCAGTTGGATAACGATTGTCGTGCCTCTGCTCACTTTTGAGGTCCTGCTCGTTCACAGATTGGATGGCCACAATACA
TTCTCCTACGTCTCCATATTTGTTCCCCTTTGGCTTTCCTTACTAACTTTAATGGCCACAACATTTAGGCGAAAGGGGGG
CAATCATTGGTGGTTTGGCATTCGCAGAGACTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATATGGGA
ACATTTCATATGATCTCCATCACGAAGATAGTGAAGATGCTGAAGAAACATCAGTTCCAGAAGCTCCGAAAATTGCTCCA
ATATTTGGAAAGAAGGCCAGAGTAGTTATAACCCAGAGCCCTGGGAAATACGTTCCCCCCCCTCCCAAGTTAAATATTGA
TATGCCAGATTAA

Alignment

ORF - retro_pabe_118 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLRGLFQDFNPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQ
          MN.RGLFQDFNPSKFLIY.CLLLFSVLL.LRLDGIIQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.
Retrocopy MNPRGLFQDFNPSKFLIYTCLLLFSVLLPLRLDGIIQWSYWAVFAPIWLWKLLVVAGASVGAGVWARNPR

Parental  YRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
          YR.EGE.CVEFKAMLIAV.IHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
Retrocopy YRTEGEACVEFKAMLIAVVIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL

Parental  ELEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTH
          ELEILCSVNILQFIFIAL.LD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH
Retrocopy ELEILCSVNILQFIFIALKLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTH

Parental  ITMALSWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQ
          .TMA.SW.TIVVPLLTFE.LLVH.LDGHN.FS...IFVPLWLSL.TLMATTF..KGGNHWWFGIR.DFCQ
Retrocopy VTMAISWITIVVPLLTFEVLLVHRLDGHNTFSYVSIFVPLWLSLLTLMATTFRRKGGNHWWFGIRRDFCQ

Parental  FLLEIFPFLREYGNISYDLHHEDNEETEETPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
          FLLEIFPFLREYGNISYDLHHED.E..EET.VPE.PKIAP.F.KKARVVITQSPGKYV.PPPKLNI.MPD
Retrocopy FLLEIFPFLREYGNISYDLHHEDSEDAEETSVPEAPKIAPIFGKKARVVITQSPGKYVPPPPKLNIDMPD

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	5.42 RPM	7.57 RPM
SRP007412_cerebellum	3.16 RPM	5.96 RPM
SRP007412_heart	4.40 RPM	4.27 RPM
SRP007412_kidney	9.41 RPM	3.18 RPM
SRP007412_liver	4.16 RPM	1.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_118 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_118 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_104
Gorilla gorilla	retro_ggor_189
Macaca mulatta	retro_mmul_310
Mus musculus	retro_mmus_358
Rattus norvegicus	retro_rnor_6

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008637	1 retrocopy	retro_acar_65,
Ailuropoda melanoleuca	ENSAMEG00000009351	1 retrocopy	retro_amel_8,
Bos taurus	ENSBTAG00000006818	1 retrocopy	retro_btau_1,
Canis familiaris	ENSCAFG00000019103	1 retrocopy	retro_cfam_159,
Cavia porcellus	ENSCPOG00000003622	1 retrocopy	retro_cpor_5,
Dasypus novemcinctus	ENSDNOG00000011864	1 retrocopy	retro_dnov_2451,
Dipodomys ordii	ENSDORG00000015027	1 retrocopy	retro_dord_67,
Equus caballus	ENSECAG00000009399	1 retrocopy	retro_ecab_426,
Felis catus	ENSFCAG00000024483	1 retrocopy	retro_fcat_1116,
Homo sapiens	ENSG00000155984	1 retrocopy	retro_hsap_104,
Gorilla gorilla	ENSGGOG00000024268	1 retrocopy	retro_ggor_189,
Loxodonta africana	ENSLAFG00000003044	1 retrocopy	retro_lafr_898,
Microcebus murinus	ENSMICG00000004639	1 retrocopy	retro_mmur_106,
Myotis lucifugus	ENSMLUG00000001319	1 retrocopy	retro_mluc_2075,
Macaca mulatta	ENSMMUG00000002888	1 retrocopy	retro_mmul_310,
Mustela putorius furo	ENSMPUG00000011896	1 retrocopy	retro_mputfur_46,
Mus musculus	ENSMUSG00000073139	1 retrocopy	retro_mmus_358,
Nomascus leucogenys	ENSNLEG00000013487	1 retrocopy	retro_nleu_2723,
Otolemur garnettii	ENSOGAG00000016414	1 retrocopy	retro_ogar_88,
Procavia capensis	ENSPCAG00000009160	1 retrocopy	retro_pcap_260,
Pongo abelii	ENSPPYG00000020809	1 retrocopy	retro_pabe_118 ,
Pteropus vampyrus	ENSPVAG00000013822	1 retrocopy	retro_pvam_30,
Rattus norvegicus	ENSRNOG00000011047	1 retrocopy	retro_rnor_6,
Sus scrofa	ENSSSCG00000012739	1 retrocopy	retro_sscr_494,
Ictidomys tridecemlineatus	ENSSTOG00000014484	1 retrocopy	retro_itri_8,
Tursiops truncatus	ENSTTRG00000000643	1 retrocopy	retro_ttru_868,