RetrogeneDB ID: retro_rnor_1746

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:55675395..55676170(+)
• Located in intron of: ENSRNOG00000000368

Retrocopy information

• Ensembl ID: ENSRNOG00000031969
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ubxn2a
• Ensembl ID: ENSRNOG00000004950
• Aliases: None
• Description: UBX domain-containing protein 2A [Source:RefSeq peptide;Acc:NP_001102952]

Sequence

>retro_rnor_1746
ATGAAAGAAGTAGATAATCTTGACAGTATAAAAGAAGAATGGGTTTGTGAAACAGGACCTCCTGACAATCAACCCCTCAA
TGATAATCCACAAAAGGACTGTGAATATTTTGTTGACAGCCTTTTTGAGGAAGCAGAGAAGGCTGGTGCCAAATGCTTGT
CCCCCACTGAACAGAAGAAACAGGTAGATGTAAATATAAAATTGTGGAAAAATGGATTCACTGTCAATGATGATTTTAGA
AGTTACTCTGATGGTGCAAGTCAGCAGTTTCTGAACTCCATCAAAAAGGGGGAATTACCTTCAGAATTACAGGGAGTTTT
TGATAAAGATGAGGTGGATGTTAAAGTTGAAGATAAAAAAAAATGAAGTATGTATGTCTACAAAGCCTGTGTTCCAACCC
TTCTCAGGACAGGGCCACAGACTAGGAAGTGCTACACCAAGAATCATTTCTAAAGCAAAGAGTATTGAAGTTGACAATAA
AAGCACTTTGTCTGCTGTTTCACTGAACAACTTGGAACCCATCACCAGGATCCAGATCTGGTTAGCCAACGGGGAAAGGA
CTGTCCAAAGATTTAACATTTCTCATAGGGTGAGCCACATCAAAGACTTCATTGAAAAATACCAAGGAACTCAGAGAAGC
CCTCCCTTTGCCCTGGCAACAGCTCTTCCTTTCCTCAGATTTCTGGATGAGACGCTCACATTGGAAGAAGCAGACTTGCA
GAATGCTGTAATCATTCAGAGACTCCAAAAAACTGCCGAACCTTTTAGAAAACTC

Alignment

ORF - retro_rnor_1746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKEVDNLDSIKEEWVCETGPPDNQPLNDNPQKDCEYFVDSLFEEAEKAGAKCLSPTEQKKQVDVNIKLWK
          MKEVDNLDSIKEEWVCETGPPDNQPLNDNPQKDCEYFVDSLFEEAEKAGAKCLSPTEQKKQVDVNIKLWK
Retrocopy MKEVDNLDSIKEEWVCETGPPDNQPLNDNPQKDCEYFVDSLFEEAEKAGAKCLSPTEQKKQVDVNIKLWK

Parental  NGFTVNDDFRSYSDGASQQFLNSIKKGELPSELQGVFDKDEVDVKVEDKKN-EVCMSTKPVFQPFSGQGH
          NGFTVNDDFRSYSDGASQQFLNSIKKGELPSELQGVFDKDEVDVKVED....EVCMSTKPVFQPFSGQGH
Retrocopy NGFTVNDDFRSYSDGASQQFLNSIKKGELPSELQGVFDKDEVDVKVEDXXX>EVCMSTKPVFQPFSGQGH

Parental  RLGSATPRIVSKAKSIEVDNKSTLSAVSLNNLEPITRIQIWLANGERTVQRFNISHRVSHIKDFIEKYQG
          RLGSATPRI.SKAKSIEVDNKSTLSAVSLNNLEPITRIQIWLANGERTVQRFNISHRVSHIKDFIEKYQG
Retrocopy RLGSATPRIISKAKSIEVDNKSTLSAVSLNNLEPITRIQIWLANGERTVQRFNISHRVSHIKDFIEKYQG

Parental  TQRSPPFALATALPFLRFLDETLTLEEADLQNAVIIQRLQKTAEPFRKL
          TQRSPPFALATALPFLRFLDETLTLEEADLQNAVIIQRLQKTAEPFRKL
Retrocopy TQRSPPFALATALPFLRFLDETLTLEEADLQNAVIIQRLQKTAEPFRKL

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
SRP017611_brain	0.72 RPM	3.45 RPM
SRP017611_kidney	0.14 RPM	6.56 RPM
SRP017611_liver	0.20 RPM	3.77 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1746 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1746 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1746 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,