RetrogeneDB ID: retro_ecab_825

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 5:22583309..22583820(+)
• Located in intron of: ENSECAG00000007173

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT2
• Ensembl ID: ENSECAG00000010932
• Aliases: None
• Description: 1-acylglycerol-3-phosphate O-acyltransferase 2 [Source:HGNC Symbol;Acc:325]

Sequence

>retro_ecab_825
ATCATCGGTTGATTCATCCAGCCCTTCAAGTACATTTATGGCCTTCACTTTGAGATCAAGGGCCCCCAGAAGCTGGAGGT
GGACAAGCCCTGTGTCATCATTTCAACTACCAGAGCATCCTGATGTGATGGGCCTCATGGAGGACCTTTCCAAGCACTGT
GTGCAGGTTGCCAAGTGAGAGCTGCTCTTCCTGGGGCCCGTGGGCCTAACCATGTACCTCGGAGGCATCTTCTTCATCAA
CTGGCAGAGCTTTAGCACCGCTGTGACCGTGATGGCCAGATGTAGGCCAGCATATGGTCAGGGAAAACCTCAAAGTGTGG
ATCTATGCAGAGGGCCCATGGAAAGACAATGAGGACCTGCTGCCTTTCAAGAAATGTGCCTTCTACCTGGTGATCCAGGC
CCAGGTGCCCATCATCCCCGTGGTTGCTCCACCTGGTCCTCTTTCTACAGCTCCATGGTAAAGCTCTTCACCTCAGGAAC
AGTCAAGGTGGAAGTGCTGAACCCCATCCCC

Alignment

ORF - retro_ecab_825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 78.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IISWFVRSFKYAYGLRFEIKGRGKLEVDHPCVIIS-NHQSIL-DMMGLMEILPPRCIQIAKRELLFLGPL
          II..F...FKY.YGL.FEIKG..KLEVD.PCVIIS.N.QSIL.D.MGLME.L...C.Q.AK.ELLFLGP.
Retrocopy IIG*FIQPFKYIYGLHFEIKGPQKLEVDKPCVIIS<NYQSIL<DVMGLMEDLSKHCVQVAK*ELLFLGPV

Parental  GLIMYLGGVVFINRQRSSTAMTVMA-DVGEHLVREDLKVWIYPEGTRNDNGDLLPFKKGAFHLAIQAQVP
          GL.MYLGG..FIN.Q..STA.TVMA.DVG.H.VRE.LKVWIY.EG...DN.DLLPFKK.AF.L.IQAQVP
Retrocopy GLTMYLGGIFFINWQSFSTAVTVMA>DVGQHMVRENLKVWIYAEGPWKDNEDLLPFKKCAFYLVIQAQVP

Parental  IIPVV-YSSFSSFYNSRTKLFTSGTVKVEVLDAIP
          IIPVV..S..SSFY.S..KLFTSGTVKVEVL..IP
Retrocopy IIPVV<CSTWSSFYSSMVKLFTSGTVKVEVLNPIP

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	97.64 RPM
SRP021940_cerebellum	0.00 RPM	4.36 RPM
SRP021940_embryo	0.00 RPM	15.50 RPM
SRP021940_placental_villous	0.00 RPM	124.80 RPM
SRP021940_synovial_membrane	0.03 RPM	25.39 RPM
SRP021940_testis	0.00 RPM	38.56 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_825 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_825 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1838

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003965	1 retrocopy	retro_amel_982,
Canis familiaris	ENSCAFG00000019569	1 retrocopy	retro_cfam_1838,
Equus caballus	ENSECAG00000010932	1 retrocopy	retro_ecab_825 ,
Felis catus	ENSFCAG00000011607	1 retrocopy	retro_fcat_1778,
Mustela putorius furo	ENSMPUG00000011249	1 retrocopy	retro_mputfur_1160,
Ochotona princeps	ENSOPRG00000003291	1 retrocopy	retro_opri_578,
Ictidomys tridecemlineatus	ENSSTOG00000023422	1 retrocopy	retro_itri_5,