RetrogeneDB ID: retro_btau_991

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:32285754..32286297(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000013059
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.53717
• Ensembl ID: ENSBTAG00000044207
• Aliases: None
• Description: ras-related protein Rab-2B [Source:RefSeq peptide;Acc:NP_001179594]

Sequence

>retro_btau_991
GTCCACGGCTTTACAATAGGCATGGAGTTTGGGGCCCGTATGGTCAGCACTGATGGGAAACAGATCAAGCTGCAAATCTG
GGATATGTCTGGACAAGAATCCTTCCGTTCTATCACCCATTCCTGCTACAGGGGAGCAGCCAGTGCACTGCTGGTGTGCG
ACATTACAAGGCGTGAAACCTTCAACCACCTGACCTCATGGTTAGAGGTTACCCAGCAGCACTCTAGTTCCAACATGGTT
ATCAAGCTGATTGGGAAAAAGAGAGACTTAGAGTCCGGTAGGGATGTGAAGAGAGAAGGAGAAGCCTTTGCTCAGGAAAT
GGACTTATATTCATGGAAACTTCAACCAAAAGAGCCTGCAATGTTGAGGAGGCCTTCATTAACACAGCCAAAGACATTAT
AGGAAAATCAGCAGGGTTTATCTGATGCCCACAGTGAGGCAAATGGCATCAAGATTGGCCCCCAGCAGTGTATTTAAACC
TCAGTGGGACCCAGTGCCTCCCAGCGGGGCTCTCGTGACATGGGGGCTGACTGTGTCTGCTGC

Alignment

ORF - retro_btau_991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.18 %
• Parental protein coverage: 84.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VHDLTIGVEFGARMVNIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLED
          VH..TIG.EFGARMV..DGKQIKLQIWD..GQESFRSIT.S.YRGAA.ALLV.DITRRETFNHLTSWLE.
Retrocopy VHGFTIGMEFGARMVSTDGKQIKLQIWDMSGQESFRSITHSCYRGAASALLVCDITRRETFNHLTSWLEV

Parental  ARQHSSSNMVIMLIGNKSDLESRRDVKREEGEAFARE-HGLIFMETSAKTACNVEEAFINTAKEI-YRKI
          ..QHSSSNMVI.LIG.K.DLES.RDVKR.EGEAFA.E..GLIFMETS.K.ACNVEEAFINTAK.I.YRKI
Retrocopy TQQHSSSNMVIKLIGKKRDLESGRDVKR-EGEAFAQE<NGLIFMETSTKRACNVEEAFINTAKDI<YRKI

Parental  -QQGLFDVHNEANGIKIGPQQCISTPVGPSASQRGSHDMGADSGCC
          .QQGL.D.H.EANGIKIGPQQCI.T.VGPSASQRGS.DMGAD..CC
Retrocopy <QQGLSDAHSEANGIKIGPQQCI*TSVGPSASQRGSRDMGADCVCC

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	15.50 RPM
ERP005899_muscle	0.00 RPM	8.60 RPM
SRP017611_brain	0.00 RPM	37.78 RPM
SRP017611_kidney	0.00 RPM	24.60 RPM
SRP017611_liver	0.00 RPM	8.46 RPM
SRP030211_testis	0.00 RPM	59.01 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_991 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_991 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_991 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018959	1 retrocopy	retro_btau_1850,
Bos taurus	ENSBTAG00000044207	1 retrocopy	retro_btau_991 ,
Canis familiaris	ENSCAFG00000005641	1 retrocopy	retro_cfam_1510,
Choloepus hoffmanni	ENSCHOG00000000710	3 retrocopies	retro_chof_2314, retro_chof_706, retro_chof_900,
Cavia porcellus	ENSCPOG00000026575	1 retrocopy	retro_cpor_839,
Macropus eugenii	ENSMEUG00000010489	2 retrocopies	retro_meug_2160, retro_meug_91,
Myotis lucifugus	ENSMLUG00000001902	3 retrocopies	retro_mluc_1243, retro_mluc_1251, retro_mluc_2103,
Sorex araneus	ENSSARG00000004969	1 retrocopy	retro_sara_97,
Ictidomys tridecemlineatus	ENSSTOG00000001886	1 retrocopy	retro_itri_468,