RetrogeneDB ID: retro_btau_487

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:11227175..11227520(-)
• Located in intron of: ENSBTAG00000007356

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOCS2
• Ensembl ID: ENSBTAG00000005380
• Aliases: None
• Description: Molybdopterin synthase catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:A4FUY7]

Sequence

>retro_btau_487
ATGTCGAGCTTGGAGATCAGCTCCTCCGGCTTCAATCAGGAGACGAAATTGCCATTATCTCTCCCATTAGTGCAGGGTAG
TGCTTTTGAGCCACCTGGAAAAGATATGAATGAAGTTGAAGAGAAATCTAAAGATATAATAAAATTCATACCTGAGAAGC
TTTCAGTAGATGAAGTCTCACAGCTGGTGATTTCTCCACTCTGTGGCGCAATATCCCTATTTGTTGGGACTACAAGAAAT
AATTTTGAAGGGAAAAAAGTCATTAGCTTAGAGTATGAAGCATATCTACCAATGGCAGAAAATGAGATAAGAAAAATTTG
TCGTGACATTAGACAGAAATGGCCA

Alignment

ORF - retro_btau_487 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.91 %
• Parental protein coverage: 60.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSLEISSSCFNQETKLPLSLPLVEGSTFEPPGKDMNEVEEKSKDIIKFTSEKLSVDEVSQLVISPLCGA
          MSSLEISSS.FNQETKLPLSLPLV.GS.FEPPGKDMNEVEEKSKDIIKF..EKLSVDEVSQLVISPLCGA
Retrocopy MSSLEISSSGFNQETKLPLSLPLVQGSAFEPPGKDMNEVEEKSKDIIKFIPEKLSVDEVSQLVISPLCGA

Parental  ISLFVGTTRNNFEGKKVISLEYEAYLPMAENEIRKICSDMRQKWP
          ISLFVGTTRNNFEGKKVISLEYEAYLPMAENEIRKIC.D.RQKWP
Retrocopy ISLFVGTTRNNFEGKKVISLEYEAYLPMAENEIRKICRDIRQKWP

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	126.60 RPM
ERP005899_muscle	0.05 RPM	23.97 RPM
SRP017611_brain	0.00 RPM	21.06 RPM
SRP017611_kidney	0.12 RPM	165.31 RPM
SRP017611_liver	0.00 RPM	175.93 RPM
SRP030211_testis	0.02 RPM	16.59 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_487 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_487 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_487 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	ENSBTAG00000005380	1 retrocopy	retro_btau_487 ,
Cavia porcellus	ENSCPOG00000015752	2 retrocopies	retro_cpor_746, retro_cpor_748,
Macaca mulatta	ENSMMUG00000020449	1 retrocopy	retro_mmul_581,
Monodelphis domestica	ENSMODG00000019459	1 retrocopy	retro_mdom_1654,
Oryctolagus cuniculus	ENSOCUG00000011406	1 retrocopy	retro_ocun_575,
Otolemur garnettii	ENSOGAG00000011108	1 retrocopy	retro_ogar_2170,
Pteropus vampyrus	ENSPVAG00000010175	1 retrocopy	retro_pvam_633,
Ictidomys tridecemlineatus	ENSSTOG00000010607	1 retrocopy	retro_itri_241,
Tupaia belangeri	ENSTBEG00000008942	3 retrocopies	retro_tbel_1128, retro_tbel_216, retro_tbel_3310,
Tarsius syrichta	ENSTSYG00000001351	1 retrocopy	retro_tsyr_510,