RetrogeneDB ID: retro_ecab_209

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:10683466..10683880(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPHLN1
• Ensembl ID: ENSECAG00000016067
• Aliases: None
• Description: periphilin 1 [Source:HGNC Symbol;Acc:19369]

Sequence

>retro_ecab_209
GAAGAGAGACCTGTTCAGTCTGTGAAAACATCAGGAGACACTTCACCCTCAAGTTCTTCGGCAGTTCCTTCATCAAAGGT
GTTAGACAAACCCAGTAGGCTGACTGAAAAGGAACTTGCTGAGGCTGCAAACAACTGGGCTGCTGGAAACCTAGGGAAGG
CAATTGAAAGCAACTTACCTGAAATTTCTGAGTACGAGGCGGGACCCACGGCGCCATCGCTCATTGACCAGCCCGAAGGA
CCTGAGTCAAACGCAACAGATGGCACAGAATTATTCGAAGACAGTCAGCTCGCCAGTTGCTCTAAAGCAGCAGCATCAAA
AACCAAAGAGATTGAACAGGTTTATGGACAAGACTGTGAAATTTTCAGGATGGTGGCAAAAATGCTGATCGAAAAAGAGC
CTTCATTAGAAAAA

Alignment

ORF - retro_ecab_209 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 51.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KERPVQSLKTSRDTSPSSSSAVPSSKVLDKPSRLTEKELAEAASKWAAEKLEKADESNLPEISEYEAGST
          .ERPVQS.KTS.DTSPSSSSAVPSSKVLDKPSRLTEKELAEAA..WAA..L.KA.ESNLPEISEYEAG.T
Retrocopy EERPVQSVKTSGDTSPSSSSAVPSSKVLDKPSRLTEKELAEAANNWAAGNLGKAIESNLPEISEYEAGPT

Parental  APLFIDQTEEPESNATDGIELFEDSQLTSRSKAIASKTKEIEQVYRQDCETFGMVVKMLIEKDPSLEK
          AP..IDQ.E.PESNATDG.ELFEDSQL.S.SKA.ASKTKEIEQVY.QDCE.F.MV.KMLIEK.PSLEK
Retrocopy APSLIDQPEGPESNATDGTELFEDSQLASCSKAAASKTKEIEQVYGQDCEIFRMVAKMLIEKEPSLEK

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	0.65 RPM
SRP021940_cerebellum	0.16 RPM	0.26 RPM
SRP021940_embryo	0.00 RPM	12.25 RPM
SRP021940_placental_villous	0.00 RPM	9.43 RPM
SRP021940_synovial_membrane	0.00 RPM	6.97 RPM
SRP021940_testis	0.00 RPM	3.33 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_209 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_209 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_209 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010693	1 retrocopy	retro_chof_1231,
Callithrix jacchus	ENSCJAG00000017726	1 retrocopy	retro_cjac_1547,
Cavia porcellus	ENSCPOG00000012266	2 retrocopies	retro_cpor_744, retro_cpor_745,
Dasypus novemcinctus	ENSDNOG00000002007	1 retrocopy	retro_dnov_1790,
Equus caballus	ENSECAG00000016067	1 retrocopy	retro_ecab_209 ,
Mus musculus	ENSMUSG00000036167	3 retrocopies	retro_mmus_1657, retro_mmus_3561, retro_mmus_79,
Otolemur garnettii	ENSOGAG00000004012	2 retrocopies	retro_ogar_1387, retro_ogar_2103,
Tarsius syrichta	ENSTSYG00000010740	1 retrocopy	retro_tsyr_2044,