RetrogeneDB ID: retro_btau_1211

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:19259498..19260485(+)
• Located in intron of: ENSBTAG00000017566

Retrocopy information

• Ensembl ID: ENSBTAG00000024407
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSBTAG00000020345
• Aliases: None
• Description: Calponin-3 [Source:UniProtKB/Swiss-Prot;Acc:Q32L92]

Sequence

>retro_btau_1211
ATGACCCACTTCAACAAGGGCCCTTCCTATGGGCTTTCGGCCGAGGTCAAGAACAAGATTGCTTCCAAGTATGATCATCA
GGCAGAAGAAGATCTCCGCAATTGGATAGAAGAGGTGACAGGCATGAGCATTGGCGCCAACTTCCAGCTGGGCTTGAAAG
ATGGCATTATCCTCTGCGAACTCATAAACAAGCTACAGCCAGGCCCAGTGAAGAAGGTCAATGAGTCCTCATTAAACTGG
CCTCAGTTGGAGAATATCGGCAACTTTATTAAAGCTATTCAGGCTTATGGCATGAAGCCACATGACATATTTGAAGCAAA
TGATCTTTTTGAGAATGGAAACATGACCCAGGTTCAGACTACGTTGGTGGCCCTAGCAGGTCTGGCTAAAACAAAAGGAT
TCCATACAACCATTGACATTGGAGTTAAGTATGCAGAAAAACAAACAAGACGTTTTGATGAAGGAAAATTAAAAGCTGGC
CAGAGTGTAATTGGTTTGCAGATGGGAACCAACAAATGCGCCAGCCAAGCAGGTATGACAGCCTATGGGACGAGGAGGCA
CCTTTATGATCCCAAAATGCAAACTGACAAACCTTTTGATCAGACCACAATTAGCCTGCAAATGGGCACCAACAAAGGAG
CCAGCCAGGCGGGAATGTTAGCACCGGGTACCCGAAGAGACATCTACGATCAGAAGCTAACATTACAACCCGTGGACAAC
TCGACGATTTCCCTACAGATGGGTACCAACAAAGTCGCTTCCCAGAAAGGAATGAGTGTGTATGGGCTTGGGCGGCAAGT
GTATGATCCCAAATACTGTGCTGCTCCCACAGAACCTGTCATTCACAACGGAAGCCAAGGAACAGGAACCAATGGGTCAG
AAATCAGTGATAGTGATTATCAGGCAGAATACCCCGATGAATATCATGGCGAGTACCAAGATGACTACCCCAGAGATTAC
CAGTATGGTGACCAAGGCATTGATTAT

Alignment

ORF - retro_btau_1211 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.22 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGMSIGANFQLGLKDGIILCELINKLQPGSV
          MTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGMSIGANFQLGLKDGIILCELINKLQPG.V
Retrocopy MTHFNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGMSIGANFQLGLKDGIILCELINKLQPGPV

Parental  KKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDI
          KKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDI
Retrocopy KKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDI

Parental  GVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGT
          GVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGT
Retrocopy GVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGT

Parental  NKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEPV
          NKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEPV
Retrocopy NKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEPV

Parental  IHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYQDDYPRDYQYGDQGIDY
          IHNGSQGTGTNGSEISD..................YPRDYQYGDQGIDY
Retrocopy IHNGSQGTGTNGSEISDXXXXXXXXXXXXXXXXXXYPRDYQYGDQGIDY

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	0.14 RPM	17.52 RPM
ERP005899_muscle	0.11 RPM	24.81 RPM
SRP017611_brain	0.50 RPM	46.36 RPM
SRP017611_kidney	1.07 RPM	88.67 RPM
SRP017611_liver	0.23 RPM	7.10 RPM
SRP030211_testis	0.08 RPM	6.03 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1211 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1211 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1211 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211 ,
Bos taurus	ENSBTAG00000020764	1 retrocopy	retro_btau_612,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Sorex araneus	ENSSARG00000012874	1 retrocopy	retro_sara_582,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,