RetrogeneDB ID: retro_rnor_405

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:211213266..211214475(+)
• Located in intron of: ENSRNOG00000011614

Retrocopy information

• Ensembl ID: ENSRNOG00000011606
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ssb
• Ensembl ID: ENSRNOG00000007998
• Aliases: None
• Description: lupus La protein homolog [Source:RefSeq peptide;Acc:NP_112381]

Sequence

>retro_rnor_405
ATGGCTGAAAATGGAGATAACGAAAAAATGGCTGCTCTGGAGGCCAAAATCTGTCATCAAATTGAGTATTATTTTGGAGA
CTTCAATTTGCCACAAGACAAGTTTTTAAAAGAACAGATCAAATTGGATGAAGGCTGGGTATCTTTGGAAACAATGATAA
AATTCAACAGGCTAAACCGACTGACAACAGACTTTAATGTAATCGTGCAAGCATTGAGCAAATCTAAGGCAAAACTCATG
GAAGTGAGTGCAGACAAAACTAAAATTAGAAGATCACCAAGCAGACCACTCCCTGAAGTGATGGATGAGTATAAGAATGA
TGTGAAAAATAGATCTGTTTATATTAAAGGCTTCCCAACTGATGCCACCCTTGATGATATAAAAGAATGGCTAGATGATA
AAGGCCAAATACTGAATATTCAGATGAGAAGAAAATTGCACAAAACATTTAAGGGGTCAATATTTGCCGTGTTTGATAGT
ATTCAGTCTGCAAAGAAGTTTGTGGACACCCCCGGCCAGAAGTACAAAGACACTAATCTGCTAATACTCTTCAAGGAAGA
TTACTTTGCAAAAAAAAATGAAGAAAGAAAGCAGAGCAAAGTGGAAGCTAAATTAAAAGCTAAACAAGAACATGAAGGAA
GACACAAACCAGGAAGTACTGAAACAAGAGCTCTAGAAGGAAAAATGGGATGCTTACTGAAGTTTTCAGGTGACTTGGAT
GACCAGACCTGTAGAGAAGATTTACACTTCCTTTTCTCAAATCATGGTGAAATAAAATGGATTGACTTTGTCAGAGGAGC
AAAAGAGGGAATAATTCTCTTCAAAGAAAAGGCTAAGGACACACTTGAGAAAGCCAGAAGTGCAAATAATGGTAACCTAC
TGTTAAGGAACAAAAAGATGACTTGGAAAGTACTAGAAGGACATGCAGAAAAAGATGCAATGAAAAAAATCACAGATGAT
CAACAAGAATCTCTGAACAAATGGAAGTCAAAAGGAGGTCATGTTCGCAGATTTAAAGGAAGAGGGAAGGGTAATAGACC
TGCTTATGCTGGGGCACCCAAAGGAAGAGGACAGTTTCAAGGAAGGAGGACAAGATTTGATGATGATGATCATCGTCGTG
GACCAATGAAAAGAGGAAGAGACGGAAGAGACAGAGAAGAACCCGCATCAGAGCATAAGAAAAGAGAGAATGGTGCTAGA
GACAAGTAG

Alignment

ORF - retro_rnor_405 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.36 %
• Parental protein coverage: 82.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAENGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLETMIKFNRLNRLTTDFNVIVQ
          MAENGDNEKMAALEAKICHQIEYYFGDFNLP.DKFLKEQIKLDEGWV.LETMIKFNRLNRLTTDFNVIVQ
Retrocopy MAENGDNEKMAALEAKICHQIEYYFGDFNLPQDKFLKEQIKLDEGWVSLETMIKFNRLNRLTTDFNVIVQ

Parental  ALSKSKANLMEVSADKTKIRRSPSRPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLDDKGQILNI
          ALSKSKA.LMEVSADKTKIRRSPSRPLPEV.DEYKNDVKNRSVYIKGFPTDATLDDIKEWLDDKGQILNI
Retrocopy ALSKSKAKLMEVSADKTKIRRSPSRPLPEVMDEYKNDVKNRSVYIKGFPTDATLDDIKEWLDDKGQILNI

Parental  QMRRTLHKTFKGSIFAVFDSIQSAKKFVDTPGQKYKDTNLLILFKEDYFAKKNEERKQSKVEAKLKAKQE
          QMRR.LHKTFKGSIFAVFDSIQSAKKFVDTPGQKYKDTNLLILFKEDYFAKKNEERKQSKVEAKLKAKQE
Retrocopy QMRRKLHKTFKGSIFAVFDSIQSAKKFVDTPGQKYKDTNLLILFKEDYFAKKNEERKQSKVEAKLKAKQE

Parental  HEGRHKPGSTETRALEGKMGCLLKFSGDLDDQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFKEKAKD
          HEGRHKPGSTETRALEGKMGCLLKFSGDLDDQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFKEKAKD
Retrocopy HEGRHKPGSTETRALEGKMGCLLKFSGDLDDQTCREDLHFLFSNHGEIKWIDFVRGAKEGIILFKEKAKD

Parental  ALEKARSANNGNLLLRNKKVTWKVLEGHAEKDAMKKITDDQQESLNKWKSKGGHAARRFKG
          .LEKARSANNGNLLLRNKK.TWKVLEGHAEKDAMKKITDDQQESLNKWKSKGGH..RRFKG
Retrocopy TLEKARSANNGNLLLRNKKMTWKVLEGHAEKDAMKKITDDQQESLNKWKSKGGH-VRRFKG

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	0.14 RPM	63.41 RPM
SRP017611_kidney	0.07 RPM	67.41 RPM
SRP017611_liver	0.20 RPM	29.11 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_405 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_405 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_405 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007763	5 retrocopies	retro_chof_1125, retro_chof_1292, retro_chof_1380, retro_chof_185, retro_chof_2593,
Dasypus novemcinctus	ENSDNOG00000013450	1 retrocopy	retro_dnov_2038,
Echinops telfairi	ENSETEG00000004614	1 retrocopy	retro_etel_2056,
Homo sapiens	ENSG00000138385	1 retrocopy	retro_hsap_448,
Gorilla gorilla	ENSGGOG00000011507	3 retrocopies	retro_ggor_2914, retro_ggor_434, retro_ggor_791,
Gorilla gorilla	ENSGGOG00000023471	4 retrocopies	retro_ggor_2834, retro_ggor_2915, retro_ggor_433, retro_ggor_792,
Loxodonta africana	ENSLAFG00000000867	3 retrocopies	retro_lafr_698, retro_lafr_745, retro_lafr_982,
Macropus eugenii	ENSMEUG00000001650	1 retrocopy	retro_meug_1908,
Myotis lucifugus	ENSMLUG00000016316	1 retrocopy	retro_mluc_2493,
Macaca mulatta	ENSMMUG00000023051	2 retrocopies	retro_mmul_1153, retro_mmul_529,
Monodelphis domestica	ENSMODG00000008227	1 retrocopy	retro_mdom_1080,
Nomascus leucogenys	ENSNLEG00000004958	3 retrocopies	retro_nleu_1039, retro_nleu_177, retro_nleu_3011,
Otolemur garnettii	ENSOGAG00000029768	1 retrocopy	retro_ogar_1642,
Pongo abelii	ENSPPYG00000012919	3 retrocopies	retro_pabe_3408, retro_pabe_3641, retro_pabe_424,
Pan troglodytes	ENSPTRG00000012620	1 retrocopy	retro_ptro_2509,
Rattus norvegicus	ENSRNOG00000007998	1 retrocopy	retro_rnor_405 ,
Tupaia belangeri	ENSTBEG00000009056	4 retrocopies	retro_tbel_1065, retro_tbel_1269, retro_tbel_3318, retro_tbel_4012,
Tursiops truncatus	ENSTTRG00000002152	2 retrocopies	retro_ttru_1926, retro_ttru_466,