RetrogeneDB ID: retro_ecab_876

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:30891698..30892223(+)
• Located in intron of: ENSECAG00000005303

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSECAG00000009065
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_ecab_876
CGTGCTGACCAACAGAACAGGATCAGGGCATTTGTCGCCATTGGGGAATACAAGGGACGTGTCAGTATGGGGGTTAAGTG
CTCCAAGGCGGTAGCCACTGCCATTTGTGGGGCCGTTCTTCTGGCTAAGCTCTCTCTAGTCCCAGTGCAGTGAGGCTGCT
GGGGAAACAAGATCAGCAAGCTCCACACCATCCCTTGCAAGGCGACTGGCTGATGTGGTTCTGTGCAGGCGCACCTCAGC
CCCGCCCCCGGGGCACTGGTGTTGTCGCAGCCCTGTGCCCAAGAAGCTACTGCTGCTGACTCGCATTGACACCTGTTACA
CCTCGGCCAGGGCTGCACTGCTACCTGGGCAGCTTTGCCAAGGCCACTTTTGATGCCATTTCTAAGACCTACGGCTTTCT
CACCCCCAACCCCTGGAAAGAGACCGTGTTCACCAAGTCCCTGATCAGGAATTCACTGGCCATTTTGTAAAGACCCACCT
AGAGTTTCCGTGCAGAAGACCCAGGCTCCAGCTGTGGCCAGCACA

Alignment

ORF - retro_ecab_876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.58 %
• Parental protein coverage: 60.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RAGQRTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTG
          RA.Q..R..AFVAIG.Y.G.V..GVKCSK.VATAI.GA..LAKLS.VPV..G.WGNKI.K.HT.PCK.TG
Retrocopy RADQQNRIRAFVAIGEYKGRVSMGVKCSKAVATAICGAVLLAKLSLVPVQ*GCWGNKISKLHTIPCKATG

Parental  RCGSVLVRLIPA-PRGTGIVSA-PVPKKLLMMAGIDDCYTSAR-GCTAT-LGNFAKATFDAISKTYSYLT
          .CGSV...L.PA.PRGTG.V.A.PVPKKLL....ID.CYTSAR.GCTAT.LG.FAKATFDAISKTY..LT
Retrocopy *CGSVQAHLSPA<PRGTGVVAA<PVPKKLLLLTRIDTCYTSAR<GCTAT<LGSFAKATFDAISKTYGFLT

Parental  PDLWKETVFTKS-PYQEFTDHLVKNH-TRVSVQRTQAPAVATT
          P..WKETVFTKS.P.QEFT.H.VK.H..RVSVQ.TQAPAVA.T
Retrocopy PNPWKETVFTKS<PDQEFTGHFVKTH<PRVSVQKTQAPAVAST

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	0.12 RPM	1345.23 RPM
SRP021940_cerebellum	0.31 RPM	357.55 RPM
SRP021940_embryo	0.82 RPM	851.49 RPM
SRP021940_placental_villous	0.24 RPM	688.28 RPM
SRP021940_synovial_membrane	0.66 RPM	1087.71 RPM
SRP021940_testis	0.00 RPM	354.05 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_876 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_876 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Canis familiaris	ENSCAFG00000019472	19 retrocopies	retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Equus caballus	ENSECAG00000009065	7 retrocopies	retro_ecab_1025, retro_ecab_1105, retro_ecab_509, retro_ecab_632, retro_ecab_876 , retro_ecab_892, retro_ecab_949,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148,
Pteropus vampyrus	ENSPVAG00000016704	8 retrocopies	retro_pvam_1395, retro_pvam_1486, retro_pvam_221, retro_pvam_240, retro_pvam_34, retro_pvam_459, retro_pvam_521, retro_pvam_595,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,