RetrogeneDB ID: retro_ecab_770

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 31:19580849..19582035(-)
• Located in intron of: ENSECAG00000019757

Retrocopy information

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

Parental gene information

• Parental gene symbol: PNPLA8
• Ensembl ID: ENSECAG00000012878
• Aliases: None
• Description: patatin-like phospholipase domain containing 8 [Source:HGNC Symbol;Acc:28900]

Sequence

>retro_ecab_770
TCACTGAAACCACAGAAAGAGACATCGAGGATAAGCGGGGACTACTGTCTTGATGACCAAACTTGGGCGTTAGGTCAAGC
ACTGAGGACACCTGATTCAAAGCTCTGCATTAACAGGGTTGAAGAACTTGACTTTTCATCTTCCAGAACTTCCTGAAGGA
AAAGGAGTGGCTTCCAAGGAAAGAATTACTCCATATTTATTATGACTGAGACAAATTAAGGATGGCACTCTTCAGGCTGC
AGTGACAGAAATTTTGGCCTTAATTGGCTATGCAAATCCAGCGAAAGGAAGAGGTATCTGAATTCTCACAATTGATGACG
GAGGAGCGAGGGATGCAGTTGCTCTTCAGATATGGTGAAAGTCAGTTCAACGCACTCGAAAGCCAGCTGTCAGCTCTTTG
ATTGCATTTCTGGTGTAAGCACAGGTGCCATATTAGCTTTCATGTTGGGATTGTTTCATATGCCCCTGGACAAACATGAG
GCAGTTATTATAAATTAGGATCACATGTGTTTTCACAAAATATTGCTGTTGGAATGGTCAAAATGAGCTGGAGCCATGCA
TTTTATGACCGTCAAATGTGGGGAATTTTCTTAAGGATAGAATGGGATATGCACTCATGATTGAAACAGCAAGAAGTCCA
TATGTCCAAAGGTAGCAGCATCAAGTCCCATGGTATAAAGTGGGGTAATGCCAAAAGTTTGCAGGTTCAGAAACTATGCT
CACCCTCCTGAAGTCAACTCTCACTGTTTGGGAGGCTGTCAGTATAAACTGTGGCAGGCCACTAGAGCTCCACCTGCTGC
TTCAGGCTACTGTGCAGAGTGTGCTTTTGGGAAACGATCCCCATCAAGATGGAGGTTTTCTTCTGAATAACCTTTCAGCA
TTAGCAATGCATGAGTGTAAGTGTTGGCCAGACGTCCCATTAGAGTGCATAGCATCCCTGGGCATTGGATGTTATGAGTA
TATGAGAAGCACCATGATATACATGAGCTTGAAAACCACACAGCCTAATGTCATCAACAGTGCTACAGATATAGAAGTCC
ATGTAATACTCGATAACCTATTACCTCCTGACACTTATTTCAGATTCAGTCCTGTATTGTGTGAAAACATATCTCTAGAT
GAAAGTCTAAATGAAAAACTTTATCAGATGCAGTTGGAACGGTTGAAGTACATAGAAAGCAATGAA

Alignment

ORF - retro_ecab_770 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.97 %
• Parental protein coverage: 51.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SLQREKASYSIIARVSIDNRTRALVQALRRTTDPKLCINRVEEL-TFHLLEFPEGKGVAVKEKIIPCLLR
          SL...K....I......D..T.AL.QALR.T.D.KLCINRVEEL.TFHL.E.PEGKGVA.KE.I.P.LL.
Retrocopy SLKPQKETSRISGDYCLDDQTWALGQALR-TPDSKLCINRVEEL>TFHLPELPEGKGVASKERITPYLL*

Parental  LRQIKDETLQAAVREILALIGYVDPVKGRGIRILAIDGGGTRGVVALQTLRKLVELTQKPV-HQLFDYIC
          LRQIKD.TLQAAV.EILALIGY..P.KGRGI.IL.ID.GG.R..VALQ...K.V..T.KP...QLFD.I.
Retrocopy LRQIKDGTLQAAVTEILALIGYANPAKGRGI*ILTIDDGGARDAVALQIW*KSVQRTRKPA<CQLFDCIS

Parental  GVSTGAILAFMLGLFHMPLDECEEL-YRKLGSDVFSQNVIVGTVKMSWSHAFYDSQTW-ENILKDRMGSS
          GVSTGAILAFMLGLFHMPLD..E...Y.KLGS.VFSQN..VG.VKMSWSHAFYD.Q.W..N.LKDRMG..
Retrocopy GVSTGAILAFMLGLFHMPLDKHEAV<YYKLGSHVFSQNIAVGMVKMSWSHAFYDRQMW<GNFLKDRMGYA

Parental  LMIETARNP-TCPKVAAVSTIVNRGITPKAFVFRNYGHFPGINSHYLGGCQYKMWQAIRASSAAPGYFEE
          LMIETAR.P..CPKVAA.S..V..G..PK...FRNY.H.P..NSH.LGGCQYK.WQA.RA..AA.GY..E
Retrocopy LMIETARSP<ICPKVAASSPMV*SGVMPKVCRFRNYAHPPEVNSHCLGGCQYKLWQATRAPPAASGYCAE

Parental  YA-LGNDLHQDGGLLLNNPSALAMHECKCLWPDVPLECIVSLGTGRYESDVRNAVTYTSLKTKLSNVINS
          .A.LGND.HQDGG.LLNN.SALAMHECKC.WPDVPLECI.SLG.G.YE...R....Y.SLKT...NVINS
Retrocopy CA>LGNDPHQDGGFLLNNLSALAMHECKC-WPDVPLECIASLGIGCYEY-MRSTMIYMSLKTTQPNVINS

Parental  ATDTEEVHIMLDGLLPPDTYFRFNPVMCENIPLDESRNEKLDQLQLEGLKYIERNE
          ATD..EVH..LD.LLPPDTYFRF.PV.CENI.LDES.NEKL.Q.QLE.LKYIE.NE
Retrocopy ATDI-EVHVILDNLLPPDTYFRFSPVLCENISLDESLNEKLYQMQLERLKYIESNE

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	8.44 RPM
SRP021940_cerebellum	0.00 RPM	8.57 RPM
SRP021940_embryo	0.00 RPM	19.49 RPM
SRP021940_placental_villous	0.00 RPM	18.23 RPM
SRP021940_synovial_membrane	0.00 RPM	9.64 RPM
SRP021940_testis	0.00 RPM	17.39 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_770 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_770 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_770 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012878	1 retrocopy	retro_ecab_770 ,