RetrogeneDB ID: retro_btau_264

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:80940146..80940851(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000006872
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STARD3NL
• Ensembl ID: ENSBTAG00000038795
• Aliases: None
• Description: MLN64 N-terminal domain homolog [Source:RefSeq peptide;Acc:NP_001068895]

Sequence

>retro_btau_264
ATGAACCCCCTGCCAGAAGACATGGAGAATATGCTCATGGGGAGTCAGAGCTCACACGCTTCTGTGCACGACGTCCACTC
CATCAACCCCACGCAGCTCATGGCCAGGATCGAGTCCTATGAAGGAAGGGAGAAGAAGGGCATATCTGATGTCAGGAGGA
CTTTCTGTTTGTTTGTCACCTTTGACCTCTTATTTGTAACATCACTGTGGATAATAGAGTTAAATGTGAATGGAGGTATT
GAGAACACGTTAGAGAAAGAGGTGGTACAGTATGATTACTACTCTTCTTATTTTGATATATTTCTTTTGGCAGTTTTTCG
ATTTAAAGTGTTAATACTTGCATATGCAGTGTGCAGACTGCGCCATTGGTGGGACATAGCGTTGACAACAGCAGTGACCA
GTGCCTTTTTATTAGCAAAAGTGATCCTCTCAAAGCTTTTCTCACAAGGGGCTTTTGGCTATGTGCTGCCCATCATTTCC
TTCATCCTTGCCTGGATCGAGACATGGTTCCTGAACTTCAAAGTGTTACCTCAAGAGGCAGAAGAAGAAAACAGACTCTT
GATAGTTCAGGATGCCTCGGAGAGGGTGGCACTGATTCCTGGGGGTCTTTCTGATGGTCAGTTTTATTCTCCTCCTGAAT
CTGAAGCAGGATCTGAAAATGAAGCTGAAGAAAAGCAGGACAGTGAAAAACCACCTTTAGGACTA

Alignment

ORF - retro_btau_264 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPLPEDMENTLTGSQSSHASVRDVHSINPTQLMARIESYEGREKKGISDVRRTFCLFVTFDLLFVTLLW
          MNPLPEDMEN.L.GSQSSHASV.DVHSINPTQLMARIESYEGREKKGISDVRRTFCLFVTFDLLFVT.LW
Retrocopy MNPLPEDMENMLMGSQSSHASVHDVHSINPTQLMARIESYEGREKKGISDVRRTFCLFVTFDLLFVTSLW

Parental  IIELNVNGGIENTLEKEVVQYDYYSSYFDIFLLAVFRFKVLILAYAVCRLRHWWAIALTTAVTSAFLLAK
          IIELNVNGGIENTLEKEVVQYDYYSSYFDIFLLAVFRFKVLILAYAVCRLRHWW.IALTTAVTSAFLLAK
Retrocopy IIELNVNGGIENTLEKEVVQYDYYSSYFDIFLLAVFRFKVLILAYAVCRLRHWWDIALTTAVTSAFLLAK

Parental  VILSKLFSQGAFGYVLPIISFILAWIETWFLDFKVLPQEAEEENRLLIVQDASERAALIPGGLSDGQFYS
          VILSKLFSQGAFGYVLPIISFILAWIETWFL.FKVLPQEAEEENRLLIVQDASER.ALIPGGLSDGQFYS
Retrocopy VILSKLFSQGAFGYVLPIISFILAWIETWFLNFKVLPQEAEEENRLLIVQDASERVALIPGGLSDGQFYS

Parental  PPESEAGSENEAEEKQDSEKPLLEL
          PPESEAGSENEAEEKQDSEKP.L.L
Retrocopy PPESEAGSENEAEEKQDSEKPPLGL

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	7.21 RPM
ERP005899_muscle	0.00 RPM	5.70 RPM
SRP017611_brain	0.05 RPM	19.96 RPM
SRP017611_kidney	0.00 RPM	17.25 RPM
SRP017611_liver	0.00 RPM	2.64 RPM
SRP030211_testis	0.07 RPM	11.55 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_264 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_264 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033345	3 retrocopies	retro_btau_1248, retro_btau_743, retro_btau_744,
Bos taurus	ENSBTAG00000038795	1 retrocopy	retro_btau_264 ,
Choloepus hoffmanni	ENSCHOG00000008990	1 retrocopy	retro_chof_984,
Callithrix jacchus	ENSCJAG00000012622	1 retrocopy	retro_cjac_3042,
Cavia porcellus	ENSCPOG00000004394	1 retrocopy	retro_cpor_1237,
Dasypus novemcinctus	ENSDNOG00000017960	1 retrocopy	retro_dnov_2389,
Equus caballus	ENSECAG00000005250	1 retrocopy	retro_ecab_709,
Microcebus murinus	ENSMICG00000000945	1 retrocopy	retro_mmur_388,
Macaca mulatta	ENSMMUG00000023659	1 retrocopy	retro_mmul_2643,
Ictidomys tridecemlineatus	ENSSTOG00000014750	1 retrocopy	retro_itri_286,
Tursiops truncatus	ENSTTRG00000004099	1 retrocopy	retro_ttru_864,