RetrogeneDB ID: retro_btau_1500

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:74038377..74038729(-)
• Located in intron of: ENSBTAG00000019366

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPZ1
• Ensembl ID: ENSBTAG00000005384
• Aliases: None
• Description: Coatomer subunit zeta-1 [Source:UniProtKB/Swiss-Prot;Acc:P35604]

Sequence

>retro_btau_1500
ATGCAGGTGCTGATTTTGGAACCCTTCCTGTATACTGGTCAAAGACATCTTTATTCTGGACAATGAAGGAGATCAACTTT
TTGCCACGTACAATGACACCTATACCAGCATCAAGAAGCAAAAGGCCTTTGAGAAGAATATTTTCAACAAGACCCATAGG
ATTGACAGTGAAGCTGCCCTTTTAGAAAGCCTGAAAGTGGTATACAAAAGCTGTATCAATCTCTATTTCTGTATGATTGG
CAGCTCCTATAAAAATGAGCTGAAGTTCATGGCTGTTTTGAACTGCTTCTTCAACTAATTGAGATCAGATGCTGAGGGAA
AATGTAGAAAGCAAGCTCTGCTGGTGAACATT

Alignment

ORF - retro_btau_1500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.25 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEALILEPSLYT-VKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKTHRTDSEIALLEGLTVVY
          M..LILEP.LYT.VK.I.ILDN.GD.LFA.Y..DTY.S.K.QKAFEKNIFNKTHR.DSE.ALLE.L.VVY
Retrocopy MQVLILEPFLYT>VKDIFILDNEGDQLFATY-NDTYTSIKKQKAFEKNIFNKTHRIDSEAALLESLKVVY

Parental  KSSIDLYFYVIGSSYENELMLMTVLNCLFDSL-SQMLRKNVE-KRALLENM
          KS.I.LYF..IGSSY.NEL..M.VLNC.F..L..QMLR.NVE.K.ALL.N.
Retrocopy KSCINLYFCMIGSSYKNELKFMAVLNCFFN*L>DQMLRENVE<KQALLVNI

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	0.00 RPM	34.89 RPM
ERP005899_muscle	0.00 RPM	115.66 RPM
SRP017611_brain	0.00 RPM	35.08 RPM
SRP017611_kidney	0.00 RPM	65.55 RPM
SRP017611_liver	0.00 RPM	74.83 RPM
SRP030211_testis	0.01 RPM	43.15 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1500 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1500 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005384	1 retrocopy	retro_btau_1500 ,
Canis familiaris	ENSCAFG00000006536	1 retrocopy	retro_cfam_30,
Callithrix jacchus	ENSCJAG00000018887	2 retrocopies	retro_cjac_1771, retro_cjac_3951,
Echinops telfairi	ENSETEG00000013499	1 retrocopy	retro_etel_1782,
Microcebus murinus	ENSMICG00000008401	1 retrocopy	retro_mmur_757,
Mus musculus	ENSMUSG00000060992	1 retrocopy	retro_mmus_2439,
Oryctolagus cuniculus	ENSOCUG00000013364	2 retrocopies	retro_ocun_1511, retro_ocun_797,
Rattus norvegicus	ENSRNOG00000036835	1 retrocopy	retro_rnor_2209,
Tupaia belangeri	ENSTBEG00000008730	1 retrocopy	retro_tbel_3749,
Tursiops truncatus	ENSTTRG00000001654	2 retrocopies	retro_ttru_114, retro_ttru_856,