RetrogeneDB ID: retro_ecab_769

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 31:15962474..15963079(-)
• Located in intron of: ENSECAG00000001166

Retrocopy information

• Ensembl ID: ENSECAG00000022621
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSECAG00000021615
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]

Sequence

>retro_ecab_769
ATGGAGTACCTCATCGGCATCCAGGGCCCCGACTATGTCCTTGTTGCCTCCGTCCCGGTGGCCGCTTGCAATATTGTCCA
GATGAAGGACGATCATGACAAGATGTTTAAGATGAGTGAAAAAATCTTACTCCTATGTGTTGGAGAGGCTGGAGACACTG
CACAGTTTGCAGAATATATTCAGAAAAATTTGCAACTTTACAAGATGCGAAATGGTTATGAATTGTCTCCCACAGCAGCA
GCTAATTTCACACGCCGAAACCTGGCTGACTGTCTCCGGAGTCGGACTCCATATCATATCAACCTCCTCCTGGCTGGCTA
CAATGAGCATGAGGCGCTCCAGCTCTCTACTACATGGACTACCTGGCCGCCTTGGCCAAGGCCCCTTTCGCAGCCCACGG
CTATGGTGCCTTTCTGACTCTCAGTATCCTGGACCGATACTACACACCAACTCTCTCACGTGAGAGGGCAGTGGAGCTTC
TTAGGAAATGTCTAGAGGAGCTCCAGAAACACTTCATCCTGAATCTGCCAGCCTTCAGTGTTCGAATCATTGACAAAAAT
GGCATTCACAAGCTAGACAACATTTCTTTTCCTAAACATGGCTCC

Alignment

ORF - retro_ecab_769 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMR
          MEYLIGIQGPDYVLVAS..VAA.NIVQMKDDHDKMFKMSEKILLLCVGEAGDT.QFAEYIQKN.QLYKMR
Retrocopy MEYLIGIQGPDYVLVASVPVAACNIVQMKDDHDKMFKMSEKILLLCVGEAGDTAQFAEYIQKNLQLYKMR

Parental  NGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHE-GPALYY-MDYLAALAKAPFAAHGYGAFL
          NGYELSPTAAANFTRRNLADCLRSRTPYH.NLLLAGY.EHE.G....Y.MDYLAALAKAPFAAHGYGAFL
Retrocopy NGYELSPTAAANFTRRNLADCLRSRTPYHINLLLAGYNEHE<GAPALYYMDYLAALAKAPFAAHGYGAFL

Parental  TLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPAFSVRIIDKNGIHELDNISFPKHGS
          TLSILDRYYTPT.SRERAVELLRKCLEELQK.FILNLPAFSVRIIDKNGIH.LDNISFPKHGS
Retrocopy TLSILDRYYTPTLSRERAVELLRKCLEELQKHFILNLPAFSVRIIDKNGIHKLDNISFPKHGS

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
SRP021940_articular_cartilage	1.24 RPM	18.18 RPM
SRP021940_cerebellum	0.21 RPM	26.02 RPM
SRP021940_embryo	0.31 RPM	44.47 RPM
SRP021940_placental_villous	0.24 RPM	37.86 RPM
SRP021940_synovial_membrane	1.29 RPM	25.23 RPM
SRP021940_testis	3.71 RPM	102.31 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_769 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_769 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_769 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000715	1 retrocopy	retro_amel_743,
Canis familiaris	ENSCAFG00000003543	1 retrocopy	retro_cfam_1291,
Callithrix jacchus	ENSCJAG00000001547	1 retrocopy	retro_cjac_2110,
Dasypus novemcinctus	ENSDNOG00000017663	1 retrocopy	retro_dnov_159,
Equus caballus	ENSECAG00000021615	1 retrocopy	retro_ecab_769 ,
Echinops telfairi	ENSETEG00000019511	1 retrocopy	retro_etel_1529,
Felis catus	ENSFCAG00000030845	1 retrocopy	retro_fcat_1803,
Macropus eugenii	ENSMEUG00000000421	1 retrocopy	retro_meug_1235,
Monodelphis domestica	ENSMODG00000017902	1 retrocopy	retro_mdom_79,
Mustela putorius furo	ENSMPUG00000014891	1 retrocopy	retro_mputfur_1550,
Ochotona princeps	ENSOPRG00000012259	2 retrocopies	retro_opri_76, retro_opri_762,
Pteropus vampyrus	ENSPVAG00000001871	1 retrocopy	retro_pvam_909,
Sorex araneus	ENSSARG00000000409	2 retrocopies	retro_sara_557, retro_sara_660,
Sarcophilus harrisii	ENSSHAG00000016996	1 retrocopy	retro_shar_794,
Tupaia belangeri	ENSTBEG00000005230	1 retrocopy	retro_tbel_4039,
Tarsius syrichta	ENSTSYG00000005648	2 retrocopies	retro_tsyr_403, retro_tsyr_912,