RetrogeneDB ID: retro_ecab_426

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:10975357..10976407(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000001439
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM185B
• Ensembl ID: ENSECAG00000009399
• Aliases: None
• Description: transmembrane protein 185B [Source:RefSeq peptide;Acc:NP_001229250]

Sequence

>retro_ecab_426
ATGAACCCCAGGGGCCTGTTCCAGGACTTCAACCCGAGTAAGTTTCTCATCTACGCCTGCCTGCTGCTCTTCTCGGTGCT
GCTGCCCCTCCGCCTGGACGGCATCATCCAGTGGAGCTACTGGGCTGTCTTCGCCCCCATATGGCTGTGGAAGCTCCTGG
TCATCGCCGGTGCATCGGTGGGCGCGGGCGTTTGGGCCCGAAACCCTCGCTACCGCGCCGAGGGGGAGGCGTGCGTGGAG
TTCAAAGCTATGTTGATCGCCGTGGGCATTCACCTGCTGCTGCTCATGTTCGAAGTCCTGGTCTGCGACAGGGTGGAGAG
GGGGACCCACTTCTGGCTGCTCGTCTTCATGCCGCTCTTTTTCGTATCCCCCGTGTCCGTGGCCGCCTGCGTATGGGGCT
TCCGACACGATAGATCGCTGGAGCTGGAGCTCTTGTGCTCTGTCAACATCCTGCAGTTCATTTTCATCGCCCTGCGGCTG
GACAGGATTATCCACTGGCCGTGGCTAGTGGTGTTCGTGCCTCTGTGGATCCTCATGTCGTTCCTTTGCCTGGTCGTCCT
CTATTACATCGTCTGGTCTCTCCTGTTCTTGCGGTCCCTGGATGTGGTTGCGGAACAGCGAAGAACACACGTGACCATGG
CCATCAGCTGGATAACGATTGTCGTGCCCTTGCTCACTTTTGAGGTTCTGCTGGTTCACAGATTGGATGGGCACAATACG
TTCTCTTATATCTCCATATTTGTCCCCCTTTGGCTTTCATTAATAACGTTAATGGCCACGACATTTAGGCGAAAAGGGGG
CAACCATTGGTGGTTTGGTATTCGCAAAGATTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATATGGGA
ACATTTCATATGATCTACATCATGAAGATAGTGAAGATGCCGAAGAAACATCGGTTCCAGAAGTTCCTAAAATCGCTCCA
ATGTTTGGAAAGAAGGCCAGGGTAGTTATAACCCAGAGCCCTGGGAAATATGTTCCCCCACCTCCCAAGCTTAATATTGA
TATGCCAGAT

Alignment

ORF - retro_ecab_426 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLRGLFQDFNPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQ
          MN.RGLFQDFNPSKFLIYACLLLFSVLL.LRLDGIIQWSYWAVFAPIWLWKL.VI.GASVG.GVWARNP.
Retrocopy MNPRGLFQDFNPSKFLIYACLLLFSVLLPLRLDGIIQWSYWAVFAPIWLWKLLVIAGASVGAGVWARNPR

Parental  YRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
          YRAEGE.CVEFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
Retrocopy YRAEGEACVEFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL

Parental  ELEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTH
          ELE.LCSVNILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH
Retrocopy ELELLCSVNILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTH

Parental  ITMALSWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQ
          .TMA.SW.TIVVPLLTFE.LLVH.LDGHN.FS.I.IFVPLWLSLITLMATTF..KGGNHWWFGIRKDFCQ
Retrocopy VTMAISWITIVVPLLTFEVLLVHRLDGHNTFSYISIFVPLWLSLITLMATTFRRKGGNHWWFGIRKDFCQ

Parental  FLLEIFPFLREYGNISYDLHHEDNEETEETPVPEPPKIAPMFRKKTRVVITQSPGKYVLPPPKLNIEMPD
          FLLEIFPFLREYGNISYDLHHED.E..EET.VPE.PKIAPMF.KK.RVVITQSPGKYV.PPPKLNI.MPD
Retrocopy FLLEIFPFLREYGNISYDLHHEDSEDAEETSVPEVPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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
SRP021940_articular_cartilage	15.23 RPM	8.56 RPM
SRP021940_cerebellum	8.46 RPM	23.32 RPM
SRP021940_embryo	23.60 RPM	12.61 RPM
SRP021940_placental_villous	14.34 RPM	17.08 RPM
SRP021940_synovial_membrane	15.10 RPM	8.04 RPM
SRP021940_testis	27.50 RPM	8.82 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_426 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_426 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_426 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1
Sus scrofa	retro_sscr_494

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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,