RetrogeneDB ID: retro_ecab_246

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:67283170..67283684(-)
• Located in intron of: ENSECAG00000021301

Retrocopy information

• Ensembl ID: ENSECAG00000001628
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANP32B
• Ensembl ID: ENSECAG00000012310
• Aliases: None
• Description: acidic (leucine-rich) nuclear phosphoprotein 32 family, member B [Source:HGNC Symbol;Acc:16677]

Sequence

>retro_ecab_246
GTTCGAGAACTTGTCCTGGACAATTGCAAATCAAACGATGGGAAAATTGAGGGCTTAACAGCTGAATTTGTGAAAGAGTT
CCTCAGTCTAATAAATGTAGGCTTGATTTTCAGTTTCAAATCTCCCCAAACTACCTAAATTGAAAAAGCTTGAGCTCAGT
GACAATAGAATCTTTGGAGGTCTGGACGTGTTAGCAGAAAAACTTCCAAATCTCACACATCTAAACTTAAGTGGAAATAA
ACTGAGAGGCATCGGCACCTTGGAACCTCTGAAAAAGTTGGACTGTCTGAAAAGCCTGGATCTGTTTAACGGTGAGGTTA
CGAACCTGAATGACTACCGAGAGAGTGTCTTCAAGCTCCTGCCCCAGCTGACCTACCTGGATGGCTATGACCGAGAGGAT
CTGGAAGCCCCCGACTCGGATGCCGAGGTGGACGGTGTGGACGAAGAAGAGGAGGACGAAGAGGATGAGGATGGTGAGGA
GGAAGAGTTTGGACATGATGGAGAAGTTGATGAA

Alignment

ORF - retro_ecab_246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.17 %
• Parental protein coverage: 73.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VRELVLDNCKSNDGKIEGLTAEFVNLEFLSLINVGLI-SVSNLPKLPKLKKLELSDNRIFGGLDMLAEKL
          VRELVLDNCKSNDGKIEGLTAEFV..EFLSLINVGLI.SVSNLPKLPKLKKLELSDNRIFGGLD.LAEKL
Retrocopy VRELVLDNCKSNDGKIEGLTAEFVK-EFLSLINVGLI>SVSNLPKLPKLKKLELSDNRIFGGLDVLAEKL

Parental  PNLTHLNLSGNKLKDISTLEPLKKLDCLKSLDLFNCEVTNLNDYRESVFKLLPQLTYLDGYDREDQEAPD
          PNLTHLNLSGNKL..I.TLEPLKKLDCLKSLDLFN.EVTNLNDYRESVFKLLPQLTYLDGYDRED.EAPD
Retrocopy PNLTHLNLSGNKLRGIGTLEPLKKLDCLKSLDLFNGEVTNLNDYRESVFKLLPQLTYLDGYDREDLEAPD

Parental  SDAEVDGVDEEEEDEEGEDEEDEE-DEDGEEEE
          SDAEVDGVDEEEEDEE.ED.E.EE...DGE..E
Retrocopy SDAEVDGVDEEEEDEEDEDGEEEEFGHDGEVDE

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	1.24 RPM	29.40 RPM
SRP021940_cerebellum	0.68 RPM	23.42 RPM
SRP021940_embryo	1.87 RPM	57.77 RPM
SRP021940_placental_villous	0.87 RPM	33.53 RPM
SRP021940_synovial_membrane	1.43 RPM	32.78 RPM
SRP021940_testis	0.51 RPM	21.42 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_246 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_246 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005149	6 retrocopies	retro_chof_1293, retro_chof_1456, retro_chof_19, retro_chof_2244, retro_chof_588, retro_chof_681,
Cavia porcellus	ENSCPOG00000020118	3 retrocopies	retro_cpor_1336, retro_cpor_493, retro_cpor_509,
Equus caballus	ENSECAG00000012310	2 retrocopies	retro_ecab_246 , retro_ecab_826,
Echinops telfairi	ENSETEG00000015514	4 retrocopies	retro_etel_2053, retro_etel_2167, retro_etel_510, retro_etel_677,
Homo sapiens	ENSG00000136938	2 retrocopies	retro_hsap_1597, retro_hsap_1603,
Myotis lucifugus	ENSMLUG00000004844	2 retrocopies	retro_mluc_1787, retro_mluc_1788,
Macaca mulatta	ENSMMUG00000012242	1 retrocopy	retro_mmul_2600,
Monodelphis domestica	ENSMODG00000003261	1 retrocopy	retro_mdom_763,
Mustela putorius furo	ENSMPUG00000006433	1 retrocopy	retro_mputfur_1392,
Mus musculus	ENSMUSG00000028333	1 retrocopy	retro_mmus_2399,
Nomascus leucogenys	ENSNLEG00000016941	1 retrocopy	retro_nleu_3009,
Otolemur garnettii	ENSOGAG00000006091	2 retrocopies	retro_ogar_1915, retro_ogar_3282,
Pongo abelii	ENSPPYG00000019430	2 retrocopies	retro_pabe_1312, retro_pabe_1316,
Pan troglodytes	ENSPTRG00000021172	3 retrocopies	retro_ptro_1073, retro_ptro_1075, retro_ptro_40,
Pteropus vampyrus	ENSPVAG00000006569	1 retrocopy	retro_pvam_699,
Sorex araneus	ENSSARG00000000804	1 retrocopy	retro_sara_549,
Tupaia belangeri	ENSTBEG00000002189	8 retrocopies	retro_tbel_1659, retro_tbel_2710, retro_tbel_2772, retro_tbel_3770, retro_tbel_3863, retro_tbel_4351, retro_tbel_4361, retro_tbel_491,
Tursiops truncatus	ENSTTRG00000010825	2 retrocopies	retro_ttru_1899, retro_ttru_341,