RetrogeneDB ID: retro_ecab_569

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:40696040..40696521(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBXN2A
• Ensembl ID: ENSECAG00000020144
• Aliases: None
• Description: UBX domain protein 2A [Source:HGNC Symbol;Acc:27265]

Sequence

>retro_ecab_569
GAATATTTTGTTAACAGCCATTGAAAGAAGCTCAGAAGATTGGTGCTAACTGCTTGTCATCCACGGAAAAGAACAGGTAA
ATGTCAGTATAAAAGATTATGGAAAAATGAATTCTAAGAGTCTAATGATTTCAGAAGTTATTCTGATGACTCAAGTCAGC
GGTTTCTGAACTCCATCAAAAAGAGGAATTACCTTTAGAGTTACATGGGATTTTTGATTAAGAAGAGGTGGATATTAAGG
CTGAAGATGAGGAACATGAAGTAGGTATGTCAATGAAGCCTATATTGCAGCCCTTCTCAGGACAGGATCACAGACTGAAA
AGCACCACACCAAAAATTTTTCTAAAGCAAAGAGTATTGAGGATGAGAATAAAGATACTCTGTCTGTTGTCCCACTAAAT
AGTCTGGAACACTTCACTAAAATACAAATCTTGTTAGCCAATTAGAAAAAGATCATCTAGAAATTTCATATTTCCCACAG
G

Alignment

ORF - retro_ecab_569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.54 %
• Parental protein coverage: 62.79 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EYFVDSLFEEAQKVGAKCLSPAEQKKQVDVSIKLWKNGFTVNDDFRSYSDGASQQFLNSIKKG-ELPLEL
          EYFV.S..............P............LWKN.F....DFRSYSD..SQ.FLNSIKK..ELPLEL
Retrocopy EYFVNSH*KKLRRLVLTACHPRKRTGKCQYK-RLWKNEF*ESNDFRSYSDDSSQRFLNSIKKR<ELPLEL

Parental  QGIFDKEEVDVKVEDKKNEVCMSTKPVFQPFSGQGHRLGSATPKI-VSKAKSFEVENKNSLSTVPLNHLE
          .GIFD.EEVD.K.ED...EV.MS.KP..QPFSGQ.HRL.S.TPKI..SKAKS.E.ENK..LS.VPLN.LE
Retrocopy HGIFD*EEVDIKAEDEEHEVGMSMKPILQPFSGQDHRLKSTTPKI<FSKAKSIEDENKDTLSVVPLNSLE

Parental  PITNIQIWLANGKRIVQKFNISHR
          ..T.IQI.LAN.K.I..KF.ISHR
Retrocopy HFTKIQILLAN*KKII*KFHISHR

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	4.49 RPM
SRP021940_cerebellum	0.00 RPM	5.82 RPM
SRP021940_embryo	0.00 RPM	7.31 RPM
SRP021940_placental_villous	0.00 RPM	9.04 RPM
SRP021940_synovial_membrane	0.00 RPM	4.61 RPM
SRP021940_testis	0.00 RPM	3.07 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_569 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_569 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_569 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569 ,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,