RetrogeneDB ID: retro_btau_89

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:69015441..69015687(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000021446
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: NEDD8
• Ensembl ID: ENSBTAG00000038842
• Aliases: None
• Description: NEDD8 precursor [Source:RefSeq peptide;Acc:NP_777189]

Sequence

>retro_btau_89
ATGCTAATTAAAGTGAAGACGCTGACCAGAAAGGAGATTGAGATTGACACTGAACCCACAGACAAGGTGGAACAAATCAA
AGAGCGTGTGAAGGAGAAAGAGGGAATTCCCCCAGAGCAGCAGAGGCTCACCTACAGTGGTAGACAGATAAACGTCAAGA
AGACATCAACTGATTACAGGCTGTTAAGTGGTTCAGTCCTCCATCTGGTATTGGCTCTGAGAGGAGGGGGTGGTCTTCGG
CAGTGA

Alignment

ORF - retro_btau_89 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VISIKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVL
          .I..KTLT.KEIEID.EPTDKVE.IKERV.EKEGIPP.QQRL.YSG.Q.N..KT..DY..L.GSVLHLVL
Retrocopy LIKVKTLTRKEIEIDTEPTDKVEQIKERVKEKEGIPPEQQRLTYSGRQINVKKTSTDYRLLSGSVLHLVL

Parental  ALRGGGGLRQ
          ALRGGGGLRQ
Retrocopy ALRGGGGLRQ

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	10.24 RPM
ERP005899_muscle	0.05 RPM	24.65 RPM
SRP017611_brain	0.00 RPM	27.45 RPM
SRP017611_kidney	0.12 RPM	31.77 RPM
SRP017611_liver	0.00 RPM	14.57 RPM
SRP030211_testis	0.00 RPM	33.00 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_89 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_89 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_89 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89 ,
Canis familiaris	ENSCAFG00000012097	1 retrocopy	retro_cfam_1789,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064,
Cavia porcellus	ENSCPOG00000010930	1 retrocopy	retro_cpor_371,
Erinaceus europaeus	ENSEEUG00000011640	2 retrocopies	retro_eeur_165, retro_eeur_43,
Echinops telfairi	ENSETEG00000018391	2 retrocopies	retro_etel_1118, retro_etel_1677,
Homo sapiens	ENSG00000129559	1 retrocopy	retro_hsap_180,
Gorilla gorilla	ENSGGOG00000016105	1 retrocopy	retro_ggor_261,
Macaca mulatta	ENSMMUG00000029409	1 retrocopy	retro_mmul_2236,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681,
Vicugna pacos	ENSVPAG00000009104	4 retrocopies	retro_vpac_270, retro_vpac_316, retro_vpac_480, retro_vpac_558,