RetrogeneDB ID: retro_btau_373

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:43935670..43936221(-)
• Located in intron of: ENSBTAG00000010103

Retrocopy information

• Ensembl ID: ENSBTAG00000046184
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.106570
• Ensembl ID: ENSBTAG00000031861
• Aliases: None
• Description: GTP-binding protein Rheb precursor [Source:RefSeq peptide;Acc:NP_001026934]

Sequence

>retro_btau_373
ATGCCGCAGTCCAAGTCCCGGAAGATCGCGATCCTGGGCTACCGGTCTGTGGGGAAATCCTCGTTGACGATTCAGTATGT
TGAAGGCCAATTTGTTGACTCCTACGATCCAACCATAGAAAATACTTTCACAAAATTGATCACAGTAAATGGACAGGAGT
ATCATCTTCAACTTGTGGACACAGCTGGGCAGGATGAATATTCCATCTTTCCTCAGACATACTCCATAGATATTAATGGC
TATATTCTTGTGTATTCTGTTACATCAATCAAAAGCTTTGAAGTGATCAAAGTTATCCATGGCAAATTGTTGGATATGGT
GGGGAAAGTACAGATACCTATTATGTTGGTTGGGAATAAGAAAGACCTACATATGGAAAGGGTGATTAGTTATGAAGAAG
GGAAAGCGTTAGCAGAGTCTTGGAACGCAGCGTTTTGGAATCATCTGCTAAAGAAAATCAGACTGCTGTTGATGTTTTTA
GAAGGATAATTTTGGAGGCAGAAAAAATCGATGGGGCCCCTTCACAAGGAAAGTCTTCCTGCTCGGTGATG

Alignment

ORF - retro_btau_373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIF
          MPQSKSRKIAILGYRSVGKSSLTIQ.VEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIF
Retrocopy MPQSKSRKIAILGYRSVGKSSLTIQYVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIF

Parental  PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES
          PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES
Retrocopy PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES

Parental  WNAAF-LESSAKENQTAVDVFRRIILEAEKIDGAASQGKSSCSVM
          WNAAF.LESSAKENQTAVDVFRRIILEAEKIDGA.SQGKSSCSVM
Retrocopy WNAAF<LESSAKENQTAVDVFRRIILEAEKIDGAPSQGKSSCSVM

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	0.50 RPM	28.41 RPM
ERP005899_muscle	0.21 RPM	20.53 RPM
SRP017611_brain	1.32 RPM	28.32 RPM
SRP017611_kidney	1.01 RPM	35.33 RPM
SRP017611_liver	0.30 RPM	19.18 RPM
SRP030211_testis	0.22 RPM	29.24 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_373 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_373 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_373 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031861	1 retrocopy	retro_btau_373 ,
Callithrix jacchus	ENSCJAG00000020414	1 retrocopy	retro_cjac_1694,
Cavia porcellus	ENSCPOG00000007541	2 retrocopies	retro_cpor_287, retro_cpor_787,
Dasypus novemcinctus	ENSDNOG00000016493	1 retrocopy	retro_dnov_2542,
Homo sapiens	ENSG00000106615	2 retrocopies	retro_hsap_568, retro_hsap_570,
Gorilla gorilla	ENSGGOG00000014675	1 retrocopy	retro_ggor_149,
Loxodonta africana	ENSLAFG00000000691	1 retrocopy	retro_lafr_471,
Macropus eugenii	ENSMEUG00000011774	1 retrocopy	retro_meug_172,
Myotis lucifugus	ENSMLUG00000004309	2 retrocopies	retro_mluc_2140, retro_mluc_857,
Mus musculus	ENSMUSG00000028945	1 retrocopy	retro_mmus_1779,
Oryctolagus cuniculus	ENSOCUG00000013173	1 retrocopy	retro_ocun_1309,
Ictidomys tridecemlineatus	ENSSTOG00000004544	2 retrocopies	retro_itri_1251, retro_itri_1357,
Tarsius syrichta	ENSTSYG00000001286	2 retrocopies	retro_tsyr_1174, retro_tsyr_1848,