RetrogeneDB ID: retro_ecab_454

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:70248343..70248886(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ACAA2
• Ensembl ID: ENSECAG00000019394
• Aliases: None
• Description: acetyl-CoA acyltransferase 2 [Source:HGNC Symbol;Acc:83]

Sequence

>retro_ecab_454
TTGAGCCAGGCTCCCTGCTGAGCCAGAAACTAGTGTGTTAGAACCATGTTTGGATCAGATCTCAAGCTGGAAGATTCTTC
GGGAGCAGCGTTAGCAGATTCCCAACTCACCATGGGAATTACTGCAGAGAATTTTGCAAAACATAAAATAAGCAGACAAG
GATGTAATGAATACACCCTGTGGTCACAGCAGAGGCTGAAAGCTGCTAATGATGCTGGTTACTTCAATAATAAGATGGTA
CCAATCAAAGTGAAGACAAGGAAAGGAAAACAGCCAATGCAAGTAGGTGAGCATGCTTGTCCCTGAGCAAGCCTGGAGCA
GTTAAATAAACTTTGGCCAATATTCAAGATAAAAGGGACTGCCACTGCAAGGAGTATATTGGGAGCATCTGATGCTTTCA
TAGCTAGTGAAGATGCTGGTAAAAAACGTAACTTCACACCACTGACAAGAATTGTGGGCTATTTTGTATCTGAATGTGAT
CCTTCTATGATGGATATCTGTCTTGTCCCTGCTATCAATGGAGCACTATAGAAAATAAGACTG

Alignment

ORF - retro_ecab_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.36 %
• Parental protein coverage: 68.12 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQAPFCVRNVRFGTRFGSDLKLEDTLWTSLTDTHVQLTMAITAENLAVKHKISREDCDKYALQSQQRWK
          .SQAP...RN....T.FGSDLKLED.....L.D...QLTM.ITAEN.A.KHKISR..C..Y.L.SQQR.K
Retrocopy LSQAPC*ARN*CVRTMFGSDLKLEDSSGAALADS--QLTMGITAENFA-KHKISRQGCNEYTLWSQQRLK

Parental  AANDAGYFNNEMAPIEVKTKKGKQIMQVDEHARPQTTLEQLSKLPPVFKKEGTVTAGNASGVCDGAGAVI
          AANDAGYFNN.M.PI.VKT.KGKQ.MQV.EHA.P...LEQL.KL.P.FK..GT.TA....G..D......
Retrocopy AANDAGYFNNKMVPIKVKTRKGKQPMQVGEHACP*ASLEQLNKLWPIFKIKGTATARSILGASD----AF

Parental  IASEDAVKKHNFTPLARIVGYFVSGCDPSLMGIGPVPAINGALKKTGL
          IASEDA.KK.NFTPL.RIVGYFVS.CDPS.M.I..VPAINGAL.K..L
Retrocopy IASEDAGKKRNFTPLTRIVGYFVSECDPSMMDICLVPAINGAL*KIRL

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	0.00 RPM	33.77 RPM
SRP021940_cerebellum	0.00 RPM	21.76 RPM
SRP021940_embryo	0.00 RPM	51.61 RPM
SRP021940_placental_villous	0.00 RPM	24.58 RPM
SRP021940_synovial_membrane	0.00 RPM	33.38 RPM
SRP021940_testis	0.00 RPM	61.39 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_454 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_454 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009411	1 retrocopy	retro_amel_602,
Equus caballus	ENSECAG00000019394	1 retrocopy	retro_ecab_454 ,
Homo sapiens	ENSG00000167315	1 retrocopy	retro_hsap_4829,
Gorilla gorilla	ENSGGOG00000012552	1 retrocopy	retro_ggor_3011,
Myotis lucifugus	ENSMLUG00000022960	1 retrocopy	retro_mluc_654,
Nomascus leucogenys	ENSNLEG00000011576	1 retrocopy	retro_nleu_2706,
Ochotona princeps	ENSOPRG00000007567	2 retrocopies	retro_opri_1224, retro_opri_348,
Pan troglodytes	ENSPTRG00000010016	1 retrocopy	retro_ptro_3214,
Vicugna pacos	ENSVPAG00000012121	1 retrocopy	retro_vpac_625,