RetrogeneDB ID: retro_btau_1

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:72356581..72357634(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000026829
• Aliases: TMEM185B, FAM11B
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM185A
• Ensembl ID: ENSBTAG00000006818
• Aliases: None
• Description: None

Sequence

>retro_btau_1
ATGAACCCCAGGGGCCTATTCCAGGACTTCAACCCGAGTAAGTTCCTCATCTACGCTTGCCTGCTGCTCTTCTCAGTGCT
GCTGCCCCTCCGACTGGACGGCGTCATCCAATGGAGCTACTGGGCCGTGTTCGCCCCCATCTGGTTGTGGAAGCTTCTGG
TCCTCGCGGGCGCCTCTGTTGGCGCGGGCGTTTGGGCGCGAAACCCGCGCTACCGCACAGAGGGAGAGGCCTGTGTGGAG
TTCAAGGCCATGCTGATCGCCGTGGGCATCCACCTGCTGCTGCTCATGTTCGAGGTCCTGGTCTGCGATCGGGTGGAGCG
CGGGACCCACTTCTGGCTGCTGGTCTTCATGCCGCTCTTCTTTGTGTCGCCCGTGTCCGTGGCCGCCTGCGTTTGGGGCT
TCCGACACGACCGGTCCCTGGAGCTGGAGATCCTGTGCTCCGTCAACATCCTGCAATTCATCTTCATCGCCCTGAGGCTG
GACCGGATCATCCACTGGCCTTGGCTGGTGGTGTTTGTGCCACTGTGGATCCTCATGTCATTCCTTTGCCTGGTAGTCCT
CTATTACATCGTTTGGTCCCTCCTGTTCCTGCGCTCCCTGGATGTGGTTGCTGAGCAGCGAAGAACCCACGTGACCATGG
CCATCTGCTGGATAACGATCGTGGTGCCGCTGCTCATTTTCGAGGTTCTGCTGGTGCACAGGCTGGATGGACACAACATG
TTTTCCTACATCTCCATATTCGTCCCCCTTTGGCTCTCATTAATCACATTAATGGCCACAACGTTTAGGCGAAAAGGGGG
CAACCATTGGTGGTTTGGTATTCGCAGAGATTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATATGGAA
ACATTTCCTATGATCTACATCATGAAGATAGTGAAGATGCTGAAGAAACATCGGCTCCAGAAGCTCCTAAAATCGCTCCA
ATGTTTGGAAAGAAGGCCAGGGTGGTGATAACACAGAGCCCTGGGAAATATGTCCCCCCACCCCCCAAGTTAAATATTGA
CATGCCTGATTAA

Alignment

ORF - retro_btau_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.54 %
• Parental protein coverage: 98.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFVIFSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQYRAEG
          LF..F.PSKFLIYACLLLFSVLL.LRLDG.IQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.YR.EG
Retrocopy LFQDFNPSKFLIYACLLLFSVLLPLRLDGVIQWSYWAVFAPIWLWKLLVLAGASVGAGVWARNPRYRTEG

Parental  ETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEIL
          E.CVEFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEIL
Retrocopy EACVEFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEIL

Parental  CSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHITMAL
          CSVNILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH.TMA.
Retrocopy CSVNILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTHVTMAI

Parental  SWMTIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEI
          .W.TIVVPLL.FE.LLVH.LDGHN.FS.I.IFVPLWLSLITLMATTF..KGGNHWWFGIR.DFCQFLLEI
Retrocopy CWITIVVPLLIFEVLLVHRLDGHNMFSYISIFVPLWLSLITLMATTFRRKGGNHWWFGIRRDFCQFLLEI

Parental  CPFLREYGNISYDLHHEGSEETEETPVPEPPKIAPMFRKKTRVVITQSPGKYVLPPPKLNIEMPD
          .PFLREYGNISYDLHHE.SE..EET..PE.PKIAPMF.KK.RVVITQSPGKYV.PPPKLNI.MPD
Retrocopy FPFLREYGNISYDLHHEDSEDAEETSAPEAPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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
ERP005899_liver	1.37 RPM	6.42 RPM
ERP005899_muscle	9.03 RPM	10.19 RPM
SRP017611_brain	11.65 RPM	18.00 RPM
SRP017611_kidney	8.77 RPM	15.88 RPM
SRP017611_liver	4.23 RPM	12.91 RPM
SRP030211_testis	14.67 RPM	6.41 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_494
Equus caballus	retro_ecab_426

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 22 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,
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,
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,
Tursiops truncatus	ENSTTRG00000000643	1 retrocopy	retro_ttru_868,