RetrogeneDB ID: retro_btau_72

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:73648526..73649642(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000016713
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TMEM30A
• Ensembl ID: ENSBTAG00000005100
• Aliases: None
• Description: cell cycle control protein 50A [Source:RefSeq peptide;Acc:NP_001068691]

Sequence

>retro_btau_72
GCACCCCGCCGGGCCGCAGCACCCGAGCGCCCCTCCGTGGGTCCGCGCGGCGCCATGACCTGGAGCGCCACCGCCCGGGG
CGCCCACCAGCCCGACAACACCGCGTTCACGCAGCAGCGCCTCCCCGCCTGGCACCCGCTGCTGTCGGCCAGCATCACGC
TGCCGCTCTTCTTCTGCGCCGGCCTGGCCTTCATAGGGCTGGGCCTGGGCCTCTACTACTCCTCCAATGGCATCAAGGAG
CTCGCGTATGACTACACCGGCGACTCGGGTACCGGCAACTGCTCGGTGTGCGCCATGGCCGGCCAGGGCCGCGCGCCGCC
GCCCCCCTGCTCGTGCGCCTGGTACTTCTCGCTGCCCGAGCTCTTCCAGGGCCCGGTGTACCTCTACTACGAGCTGACGA
ACTTCTACCAGAACAACCGGCGCTACGGCGTGTCCCGCGACGACTCGCAGCTGAGCGGGCTGCCGAGCTCGCTGCGCCAC
CCGGTCAACGAGTGCGCCCCCTACCAGTACAGCGCGGCCGGCCTGCCCATCGCGCCCTGCGGCGCCATCGCCAACAGCCT
CTTCAACGACTCCTTCTCGCTGTGGCACCAGCGCCAGCCCAACGGGCCCTACGTCGAGGTGCCGCTCGACCGCACCGGCA
TCGCCTGGTGGACCGATTACCACGTCAAGTTCCGCAACCCGCCGCTGGTGAACGGCAGCCTGGCGCTGGCCTTCCAGGGC
ACCGCGCCCCCGCCCAACTGGCACCGGCCGGTCTACGAGCTGAGCCCCGACCCCAACAACACCGGCTTCATCAACCAGGA
CTTCGTGGTGTGGATGCGCACCGCTGCGCTGCCCACGTTCCGCAAGCTGTACGCGCGCATCCGCCAGGGCAACTACTCTG
CCGGGCTGCCGCGGGGCGCCTACCGCGTCAACATCACCTATAACTACCCGGTGCGCGCCTTCAACGGCCACAAAAGCCTC
ATCTTCAGCAGCATCTCGTGGATGGGCGGCAAGAATCCATTCCTGGGCATCGCCTACCTGCTGGTCGGCTCCCTCTGCAT
CCTCGTGGGCTTTGTCATGCTGGTCGTCTACATTCGCTACCAGGACCAGAACGACGACGAGGAGGACGACGAGTGA

Alignment

ORF - retro_btau_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.65 %
• Parental protein coverage: 70.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PCVCTINFTLEQSFEGNVFMYYGLSNFYQNHRRYVKSRDDGQLNGDPSALLNPSKECEPYRRNE-DKPIA
          PC.C...F.L...F.G.V..YY.L.NFYQN.RRY..SRDD.QL.G.PS.L..P..EC.PY.......PIA
Retrocopy PCSCAWYFSLPELFQGPVYLYYELTNFYQNNRRYGVSRDDSQLSGLPSSLRHPVNECAPYQYSAAGLPIA

Parental  PCGAIANSMFNDTLELFQVGNASD-LTPIPLKKKGIAWWTDKNVKFRNPPGTD-PLEERFKGTTKPVNWV
          PCGAIANS.FND...L.............PL...GIAWWTD..VKFRNPP.....L...F.GT..P.NW.
Retrocopy PCGAIANSLFNDSFSLWHQRQPNGPYVEVPLDRTGIAWWTDYHVKFRNPPLVNGSLALAFQGTAPPPNWH

Parental  KPVYMLDSDEDNNGFINEDFIVWMRTAALPTFRKLYRLIERKNDLHPTLPAGRYYLNITYNYPVHSFDGR
          .PVY.L..D..N.GFIN.DF.VWMRTAALPTFRKLY..I.R.......LP.G.Y..NITYNYPV..F.G.
Retrocopy RPVYELSPDPNNTGFINQDFVVWMRTAALPTFRKLYARI-RQGNYSAGLPRGAYRVNITYNYPVRAFNGH

Parental  KRMILSTISWMGGKNPFLGIAYITIGSISFLLGVVLLVINHKYRNSSN
          K..I.S.ISWMGGKNPFLGIAY...GS...L.G.V.LV....Y.....
Retrocopy KSLIFSSISWMGGKNPFLGIAYLLVGSLCILVGFVMLVVYIRYQDQND

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	2.88 RPM	15.93 RPM
ERP005899_muscle	47.46 RPM	39.28 RPM
SRP017611_brain	1.00 RPM	89.44 RPM
SRP017611_kidney	10.91 RPM	76.52 RPM
SRP017611_liver	30.96 RPM	24.39 RPM
SRP030211_testis	6.30 RPM	127.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_72 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_72 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_72 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72 ,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,