RetrogeneDB ID: retro_ecab_512

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:22083803..22084409(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSECAG00000014090
• Aliases: None
• Description: ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]

Sequence

>retro_ecab_512
GAAGTCCTGCACCAGAACCTGCCCAGCGCCAGAAGTTTTGGAAGCAGTGGAGCTGCAGATCATCTTGAAGAACTATGACC
CTCAGAAGGACAAATGCTTTTCCAGCACCGTCAGGCTTAAGTCCACTCCCTGCCCCAAATTCCCCATGTGTGCCCTGGGG
GACCAGCAGCACTGTGATGAGGCCAAGGCTGTGGATATCCCCCACATGGGCATTGAGGCACTGAAGAAACTTGACAAGAA
TGAGAAGCTGGTCAAGAAGTTGGCCAAAAAGGATGACCCCTTTTAGGCTTCAGAGTCTCTGGTCAAGCAGATCCCATGAA
TCCTGGGCCCAGGCCTGAATAAAGCTGACAAGTTCCCGTCCTCGCTGACTGACAATGAGAATATGGTGGCCGAAGTTGAT
GAAGTGAAGTCCATGATTAAGTCCCAGATGAAGAAGAAGTTGCTGTGTCTAGCAGTGGATGTTGGCTACTTAAGATGACA
GATAATGAGCTTGTGTGAAACATCCACTTAGCTGTCAGTTTCCTGGTGTCATGGCTCAAGAATAACTGCCAGAAGGTCCA
GGCTTTATACGTCAAGAGCACCATGAGCAAGCCCCAATGTCTGTAC

Alignment

ORF - retro_ecab_512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.67 %
• Parental protein coverage: 93.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EVLHGN-QRKRSKF-LETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQQHCDEAKAVDIP
          EVLH.N....R.KF.LE.VELQI.LKNYDPQKDK.FS.TVRLKSTP.PKF..C.LGDQQHCDEAKAVDIP
Retrocopy EVLHQN<PAQRQKF<LEAVELQIILKNYDPQKDKCFSSTVRLKSTPCPKFPMCALGDQQHCDEAKAVDIP

Parental  HMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTHNENMVAKVDEVKS
          HM.IEALKKL.KN.KLVKKLAKK.D.F.ASESL.KQIP.ILGPGLNKA.KFPS.LT.NENMVA.VDEVKS
Retrocopy HMGIEALKKLDKNEKLVKKLAKKDDPF*ASESLVKQIP*ILGPGLNKADKFPSSLTDNENMVAEVDEVKS

Parental  TIKFQM-KKVLCLAVAVGH-VKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMGKPQRLY
          .IK.QM.KK.LCLAV.VG...KMTD.ELV.NIHLAV.FLVS.LK.N.Q.V.ALY.KSTM.KPQ.LY
Retrocopy MIKSQMKKKLLCLAVDVGY<LKMTDNELV*NIHLAVSFLVSWLKNNCQKVQALYVKSTMSKPQCLY

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	0.24 RPM	914.02 RPM
SRP021940_cerebellum	0.00 RPM	365.08 RPM
SRP021940_embryo	0.03 RPM	730.97 RPM
SRP021940_placental_villous	0.77 RPM	480.58 RPM
SRP021940_synovial_membrane	1.02 RPM	712.24 RPM
SRP021940_testis	0.13 RPM	262.42 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_512 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_512 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_512 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000014090	2 retrocopies	retro_ecab_512 , retro_ecab_517,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Mus musculus	ENSMUSG00000037805	8 retrocopies	retro_mmus_1110, retro_mmus_1304, retro_mmus_1422, retro_mmus_149, retro_mmus_1737, retro_mmus_2038, retro_mmus_2652, retro_mmus_452,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Pongo abelii	ENSPPYG00000016529	10 retrocopies	retro_pabe_1208, retro_pabe_1597, retro_pabe_2614, retro_pabe_2759, retro_pabe_3302, retro_pabe_3315, retro_pabe_3377, retro_pabe_357, retro_pabe_451, retro_pabe_475,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Sus scrofa	ENSSSCG00000001543	7 retrocopies	retro_sscr_1169, retro_sscr_1174, retro_sscr_120, retro_sscr_246, retro_sscr_379, retro_sscr_461, retro_sscr_465,