RetrogeneDB ID: retro_btau_97

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:86579143..86579452(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000009073
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CSTB
• Ensembl ID: ENSBTAG00000000524
• Aliases: None
• Description: Cystatin-B [Source:UniProtKB/Swiss-Prot;Acc:P25417]

Sequence

>retro_btau_97
AGACCCACCACTGAGATGATGTGTGGTGCACCCCCCACCAAGCAGCTGGCCGCGGCTGAGATCCAGGCCATTGCTGACAA
AGTGAAGTCTCCGCTGGAAGAGAAGGAAAACAAGAAGTTCCTGGTGTTCAATGCTGTGGAGTTCAAAAGCCAAGGGGTTG
CTGGGAGGACATTCTTCACCAAGGTTCAAATGGATGATGACTTCGTGCACATTCAAGTGTTTGAAAGCCTTCCACAGGAG
AACAAGCCAGTGGCCTTGACCAGCTACCAGATCCACAAAGGCAGACAAGACGAAGTGACGTGCTTCTAG

Alignment

ORF - retro_btau_97 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMCGGTSATQPATAETQAIADKVKSQLEEKENKKFPVFKALEFKSQLVAGKNYFIKVQVDEDDFVHIRVF
          MMCG.....Q.A.AE.QAIADKVKS.LEEKENKKF.VF.A.EFKSQ.VAG...F.KVQ.D.DDFVHI.VF
Retrocopy MMCGAPPTKQLAAAEIQAIADKVKSPLEEKENKKFLVFNAVEFKSQGVAGRTFFTKVQMD-DDFVHIQVF

Parental  ESLPHENKPVALTSYQTNKSRHDELTYF
          ESLP.ENKPVALTSYQ..K.R.DE.T.F
Retrocopy ESLPQENKPVALTSYQIHKGRQDEVTCF

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	7.93 RPM
ERP005899_muscle	0.00 RPM	42.86 RPM
SRP017611_brain	0.00 RPM	16.95 RPM
SRP017611_kidney	0.00 RPM	33.07 RPM
SRP017611_liver	0.00 RPM	11.33 RPM
SRP030211_testis	0.48 RPM	12.54 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_97 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_97 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_97 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000524	1 retrocopy	retro_btau_97 ,
Loxodonta africana	ENSLAFG00000002664	1 retrocopy	retro_lafr_370,
Myotis lucifugus	ENSMLUG00000022457	1 retrocopy	retro_mluc_379,
Macaca mulatta	ENSMMUG00000012303	1 retrocopy	retro_mmul_1609,
Otolemur garnettii	ENSOGAG00000006101	2 retrocopies	retro_ogar_3274, retro_ogar_3275,
Pteropus vampyrus	ENSPVAG00000007022	1 retrocopy	retro_pvam_1089,
Rattus norvegicus	ENSRNOG00000001201	1 retrocopy	retro_rnor_551,
Sarcophilus harrisii	ENSSHAG00000017952	3 retrocopies	retro_shar_229, retro_shar_623, retro_shar_699,