RetrogeneDB ID: retro_ecab_502

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:96242437..96243544(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSECAG00000009396
• Aliases: None
• Description: poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]

Sequence

>retro_ecab_502
ATGAATGTAGCAGCCAAGTACCGCCAGGCCTCCCTGTATGTGGGGGACCTCCATGCAGATGTCACCGAGGACCTGCTGTT
CAAGAAATTCAGCACTGTGGGGCCCGTGCTGTCCATCCGCATCTGCAGGGACCTGGTCACCCGCCGCTCTCTGGGCTATG
CCTATGTGAACTTCCTGCAGCTGGCTGATGCCCAGAAGGCCCTGGACACAATGAACTTTGACACGATCAAAGGCAAATCC
ATCCGCCTCATGTGGTCTCAACGTGACGCCTACTTAAGGAAATCTGGGATTGGGAACGTGTTCATCAAGAATCTGGACAA
ATCCATTGATAACAAAACCCTTTATGAACATTTTTCGGCCTTTGGGAAGATCCTGTCCTCCAAGGTGATGAGCGATGACC
AAGGCTCCAGGGGCTATGCGTTTGTGCACTTTCAGAACCAGATGGCCGCAGATAGGGCCATCGAGGAGATGAACGGGGCG
CTGCTTAAGGACTGCAGGCTGTTTGTTGGCAGATTCAAAAACCGCCAAGATCGGGAAGCCGAGCTCCAAAACAAAGCCAA
TGAATTCACCAATATTTACATCAAAAACTTTGGAGATGACATGGATGATAAGAGACTGGAGGAAGTTTTCAGTAAATATG
GCAAAACTGTGAGTGTTAAGGTGATGACAGACTCCACTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTTATAGCCAC
GAGGCTGCCCAAAAGGCCGTGGAAGAAATGAATGGAAAGGATATAAACGGACAGCTGCTCTTTGTAGGCCGGGCACAAAA
GAAAGCAGAGCGACAGGCTGAATTAAAGCAAATGTTTGAGCAGCAGAAACAGGAAAGATTTCGGCGGTGCCAGGGGGTGA
AGCTCTACATTAAGAACCTCGATGACACCATTGATGATGAAAAACTACGGAGGGAGTTTTCTTCCTTTGGATCAATTAGC
AGAGTCAAGGTGATGAAGGAAGAAGGGCGAAGCAAAGGCTTTGGCTTGATCTGCTTCTCCTCTCCTGAAGAGGCCACCAG
AGCAATGACTGAGATGAATGGCCGCATCTTGGGCTCCAAGCCACTCAACATCGCCCTGGCGCAGAGG

Alignment

ORF - retro_ecab_502 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.78 %
• Parental protein coverage: 56.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNAAASSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MN.AA..Y..ASLYVGDLH.DVTE..L..KFS..GPVLSIR.CRD..TRRSLGYAYVNF.Q.ADA..ALD
Retrocopy MNVAAK-YRQASLYVGDLHADVTEDLLFKKFSTVGPVLSIRICRDLVTRRSLGYAYVNFLQLADAQKALD

Parental  TMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFD.IKGK.IR.MWSQRD..LRKSG.GNVFIKNLDKSIDNK.LY..FSAFG.ILS.KV..D..GS.GY
Retrocopy TMNFDTIKGKSIRLMWSQRDAYLRKSGIGNVFIKNLDKSIDNKTLYEHFSAFGKILSSKVMSDDQGSRGY

Parental  AFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDESLKEL
          AFVHF..Q.AAD.AIE.MNG.LL.D...FVGRFK.R..REAEL..KA.EFTN.YIKNFG...DD..L.E.
Retrocopy AFVHFQNQMAADRAIEEMNGALLKDCRLFVGRFKNRQDREAELQNKANEFTNIYIKNFGDDMDDKRLEEV

Parental  FSQFGKTLSVKVMRDPSGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKVIFVGRAQKKVERQAELKRKF
          FS..GKT.SVKVM.D..GKSKGFGFVS...HE.A.KAVEEMNGK.I.G...FVGRAQKK.ERQAELK..F
Retrocopy FSKYGKTVSVKVMTDSTGKSKGFGFVSFYSHEAAQKAVEEMNGKDINGQLLFVGRAQKKAERQAELKQMF

Parental  EQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAV
          EQ.KQER..R.QGV.LYIKNLDDTIDDEKLR.EFS.FGSI...KVM.E.GRSKGFG..CFSSPEEAT.A.
Retrocopy EQQKQERFRRCQGVKLYIKNLDDTIDDEKLRREFSSFGSISRVKVMKEEGRSKGFGLICFSSPEEATRAM

Parental  TEMNGRIVGSKPLYVALAQR
          TEMNGRI.GSKPL..ALAQR
Retrocopy TEMNGRILGSKPLNIALAQR

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	0.53 RPM	87.72 RPM
SRP021940_cerebellum	0.36 RPM	38.79 RPM
SRP021940_embryo	8.03 RPM	154.79 RPM
SRP021940_placental_villous	1.88 RPM	56.96 RPM
SRP021940_synovial_membrane	1.51 RPM	102.07 RPM
SRP021940_testis	0.58 RPM	77.63 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_502 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_502 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_502 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_656
Oryctolagus cuniculus	retro_ocun_792

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Bos taurus	ENSBTAG00000017125	3 retrocopies	retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris	ENSCAFG00000003081	2 retrocopies	retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni	ENSCHOG00000005327	3 retrocopies	retro_chof_1150, retro_chof_1182, retro_chof_1274,
Equus caballus	ENSECAG00000009396	2 retrocopies	retro_ecab_2, retro_ecab_502 ,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Loxodonta africana	ENSLAFG00000000151	3 retrocopies	retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Myotis lucifugus	ENSMLUG00000012068	2 retrocopies	retro_mluc_228, retro_mluc_397,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,
Sus scrofa	ENSSSCG00000003660	3 retrocopies	retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,