RetrogeneDB ID: retro_rnor_1077

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:92831929..92832988(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004090
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Prmt1
• Ensembl ID: ENSRNOG00000026109
• Aliases: Prmt1, Hrmt1l2
• Description: Protein arginine N-methyltransferase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q63009]

Sequence

>retro_rnor_1077
ATGGCGGCAGCCGAGGCCGCGAACTGCATCATGGAGGTTTCCTGTGGCCAAGCAGAAAGTAGTGAGAAGCCCAATGCTGA
GGACATGACATCCAAAGACTACTACTTTGACTCCTATGCCCACTTTGGCATCCACGAGGAGATGCTAAAGGATGAGGTGC
GAACCCTCACGTACCGCAACTCCATGTTTCACAATCGGCATCTCTTCAAAGACAAGGTGGTGCTGGATGTGGGCTCGGGC
ACTGGCATCCTCTGCATGTTCGCTGCCAAGGCAGGGGCCCGCAAGGTCATTGGGATCGAGTGCTCCAGTATCTCTGATTA
TGCTGTGAAGATTGTCAAAGCCAACAAGTTAGACCACGTGGTGACCATCATCAAGGGCAAGGTGGAGGAGGTGGAGCTGC
CTGTGGAGAAGGTGGACATCATCATCAGCGAGTGGATGGGTTATTGCCTCTTCTATGAGTCCATGCTCAACACTGTGCTG
CACGCTCATGACAAGTGGCTGGCACCTGATGGCCTCATCTTCCCAGACCGAGCCACCCTGTATGTGACAGCCATTGAGGA
CCGACAGTATAAAGACTACAAGATCCACTGGTGGGAGAATGTATATGGCTTTGATATGTCCTGCATTAAAGACGTGGCCA
TCAAGGAGCCCCTGGTGGACGTGGTGGACCCAAAGCAGCTGGTCACCAACGCCTGCCTCATAAAGGAGGTGGACATCTAC
ACAGTCAAGGTGGAGGACCTGACCTTCACCTCCCCGTTTTGTCTGCAAGTGAAGAGGAATGACTATGTGCATGCACTAGT
GGCCTACTTCAACATCGAGTTCACCCGATGCCACAAGAGGACCGGCTTCTCTACCAGTCCTGAGTCTCCATACACACATT
GGAAGCAGACTGTGTTCTACATGGAGGACTACCTAACAGTGAAGACCGGCGAGGAGATTTTTGGCACTATTGGAATGAGG
CCCAACGCCAAAAACAATCGTGACTTGGACTTTACCATCGACCTGGACTTCAAGGGTCAGCTGTGTGAGCTCTCTTGTTC
CACCGACTACCGGATGCGC

Alignment

ORF - retro_rnor_1077 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAEAANCIMEVSCGQAESSEKPNAEDMTSKDYYFDSYAHFGIHEEMLKDEVRTLTYRNSMFHNRHLFK
          MAAAEAANCIMEVSCGQAESSEKPNAEDMTSKDYYFDSYAHFGIHEEMLKDEVRTLTYRNSMFHNRHLFK
Retrocopy MAAAEAANCIMEVSCGQAESSEKPNAEDMTSKDYYFDSYAHFGIHEEMLKDEVRTLTYRNSMFHNRHLFK

Parental  DKVVLDVGSGTGILCMFAAKAGARKVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVDI
          DKVVLDVGSGTGILCMFAAKAGARKVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVDI
Retrocopy DKVVLDVGSGTGILCMFAAKAGARKVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVDI

Parental  IISEWMGYCLFYESMLNTVLHARDKWLAPDGLIFPDRATLYVTAIEDRQYKDYKIHWWENVYGFDMSCIK
          IISEWMGYCLFYESMLNTVLHA.DKWLAPDGLIFPDRATLYVTAIEDRQYKDYKIHWWENVYGFDMSCIK
Retrocopy IISEWMGYCLFYESMLNTVLHAHDKWLAPDGLIFPDRATLYVTAIEDRQYKDYKIHWWENVYGFDMSCIK

Parental  DVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVHALVAYFNIEFTRCHKR
          DVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVHALVAYFNIEFTRCHKR
Retrocopy DVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVHALVAYFNIEFTRCHKR

Parental  TGFSTSPESPYTHWKQTVFYMEDYLTVKTGEEIFGTIGMRPNAKNNRDLDFTIDLDFKGQLCELSCSTDY
          TGFSTSPESPYTHWKQTVFYMEDYLTVKTGEEIFGTIGMRPNAKNNRDLDFTIDLDFKGQLCELSCSTDY
Retrocopy TGFSTSPESPYTHWKQTVFYMEDYLTVKTGEEIFGTIGMRPNAKNNRDLDFTIDLDFKGQLCELSCSTDY

Parental  RMR
          RMR
Retrocopy RMR

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	0.07 RPM	20.56 RPM
SRP017611_kidney	0.42 RPM	14.72 RPM
SRP017611_liver	0.00 RPM	4.10 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1077 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1077 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1077 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003670	3 retrocopies	retro_cjac_1800, retro_cjac_1979, retro_cjac_764,
Danio rerio	ENSDARG00000010246	1 retrocopy	retro_drer_7,
Felis catus	ENSFCAG00000006081	1 retrocopy	retro_fcat_1762,
Homo sapiens	ENSG00000126457	1 retrocopy	retro_hsap_3406,
Gasterosteus aculeatus	ENSGACG00000004897	1 retrocopy	retro_gacu_2,
Gorilla gorilla	ENSGGOG00000000503	1 retrocopy	retro_ggor_2305,
Macaca mulatta	ENSMMUG00000003029	1 retrocopy	retro_mmul_2121,
Otolemur garnettii	ENSOGAG00000011938	2 retrocopies	retro_ogar_2471, retro_ogar_2929,
Rattus norvegicus	ENSRNOG00000026109	2 retrocopies	retro_rnor_1077 , retro_rnor_2668,