RetrogeneDB ID: retro_rnor_1537

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:141656146..141656629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rnps1
• Ensembl ID: ENSRNOG00000008703
• Aliases: None
• Description: RNA-binding protein with serine-rich domain 1 [Source:UniProtKB/Swiss-Prot;Acc:Q6AYK1]

Sequence

>retro_rnor_1537
AAAAGAGATGAAAAAGAGAGGAACAGGTGGAGCCCTTCACCTAAACCCACCAAAGTGCACATTGGGAGGCTCACCAGGAA
TGTGACCAAGGATCATATCATGGAAATATTTTCTACTTACAGGGAAATTAAAATGATTGACATGCCTGTAGAAAGGATAC
ATCCTCATCTATCCAAAGGCTATGCGTATGTGGAATTTGAGAATCCAGATGAAGCAGAGAAGGCGCTGAAACACATGGAT
GGAGGACAAATTGATGGCCAAGAGATCACTGCCACTGCGGTGTTGGCACCCTGGCCTCGTCCACCGCCTTGGCGATTCAG
CCCGCCCAGGAGAATGCTTCCACCACCTCCCATGTGGTGTAGGTCACCTCCATTAATGAGGAGAAGGTCTTGATCCCCGA
GACGCAGGTCCCCTATGTGAAAGAGGTCTCGATCCCCCGGCCACCGCCACCACAAGAGCCGATCCAGCTCCAACTCCTCC
CAA

Alignment

ORF - retro_rnor_1537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.06 %
• Parental protein coverage: 52.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRDEKERKRRSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPD
          KRDEKER.R.SPSPKPTKVHIGRLTRNVTKDHIMEIFSTY..IKMIDMPVER.HPHLSKGYAYVEFENPD
Retrocopy KRDEKERNRWSPSPKPTKVHIGRLTRNVTKDHIMEIFSTYREIKMIDMPVERIHPHLSKGYAYVEFENPD

Parental  EAEKALKHMDGGQIDGQEITATAVLAPWPRPPPRRFSPPRRMLPPPPMWRRSPPRMRRRSRSPRRRSPVR
          EAEKALKHMDGGQIDGQEITATAVLAPWPRPPP.RFSPPRRMLPPPPMW.RSPP.MRRRS.SPRRRSP..
Retrocopy EAEKALKHMDGGQIDGQEITATAVLAPWPRPPPWRFSPPRRMLPPPPMWCRSPPLMRRRS*SPRRRSPM*

Parental  RRSRSPGRRRHRSRSSSNSSR
          .RSRSPG.R.H.SRSSSNSS.
Retrocopy KRSRSPGHRHHKSRSSSNSSQ

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	0.00 RPM	75.71 RPM
SRP017611_kidney	0.00 RPM	42.29 RPM
SRP017611_liver	0.00 RPM	21.05 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1537 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1537 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1537 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017861	1 retrocopy	retro_amel_194,
Bos taurus	ENSBTAG00000009969	7 retrocopies	retro_btau_1187, retro_btau_1239, retro_btau_1283, retro_btau_1515, retro_btau_764, retro_btau_776, retro_btau_85,
Canis familiaris	ENSCAFG00000019397	1 retrocopy	retro_cfam_449,
Choloepus hoffmanni	ENSCHOG00000004866	4 retrocopies	retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493,
Callithrix jacchus	ENSCJAG00000014969	2 retrocopies	retro_cjac_2127, retro_cjac_3377,
Cavia porcellus	ENSCPOG00000002066	2 retrocopies	retro_cpor_363, retro_cpor_953,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Felis catus	ENSFCAG00000007690	1 retrocopy	retro_fcat_248,
Homo sapiens	ENSG00000205937	1 retrocopy	retro_hsap_2911,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Myotis lucifugus	ENSMLUG00000016808	3 retrocopies	retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Macaca mulatta	ENSMMUG00000019238	1 retrocopy	retro_mmul_794,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Mus musculus	ENSMUSG00000034681	1 retrocopy	retro_mmus_173,
Oryctolagus cuniculus	ENSOCUG00000004387	2 retrocopies	retro_ocun_1544, retro_ocun_1745,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Pan troglodytes	ENSPTRG00000031310	1 retrocopy	retro_ptro_1967,
Pteropus vampyrus	ENSPVAG00000005105	1 retrocopy	retro_pvam_296,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537 , retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,
Tupaia belangeri	ENSTBEG00000009098	8 retrocopies	retro_tbel_1262, retro_tbel_1851, retro_tbel_2132, retro_tbel_2154, retro_tbel_2216, retro_tbel_3193, retro_tbel_3286, retro_tbel_4688,
Tarsius syrichta	ENSTSYG00000001629	1 retrocopy	retro_tsyr_957,
Tursiops truncatus	ENSTTRG00000008220	7 retrocopies	retro_ttru_1010, retro_ttru_1033, retro_ttru_1558, retro_ttru_1808, retro_ttru_1809, retro_ttru_203, retro_ttru_986,