RetrogeneDB ID: retro_rnor_1855

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:178862583..178862990(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050272
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Stmn1
• Ensembl ID: ENSRNOG00000016810
• Aliases: Stmn1, Lap18, OP18, PP17, PP19, PR22, SMN, prosolin
• Description: Stathmin [Source:UniProtKB/Swiss-Prot;Acc:P13668]

Sequence

>retro_rnor_1855
GCTTCAGGTCAGGCCTTTGAGCTGATTTTCACCCCCCTCCATCAAAAGAATCTGTCCCCGATTTCCCCCTTTCCCACCCC
AAAGAAGGAGGATCTTTCCCTGGAGGAAATTCAAAAGAAATTAGAAGCAGCAGAAGAAAGACGAACGTCTCATGAAGCAG
AAGTCTTGAAGCAGCTTGCTGAGACGCGGGAGCGTGAAAAAGAAGTGCCCCAGAAAGCCACTGAGAAGAACAACAACTTC
AGCAAAATGGCAAAGGAGAAACGGACCCACAAAAATCGAGGCTAATGAAGAGAACCGGGAGGTGCAATGGCTGCCGAGCT
GGAGCGTTTGCGAGAGAAGGACAAGCGTGTTGAAGAGGTGCGGAAGAACGAAGACTCCAAAGACCCTGCAGAGAGCCCGA
GGCTGAT

Alignment

ORF - retro_rnor_1855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.54 %
• Parental protein coverage: 90.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASGQAFELILSP-RSKESVPEFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLKQLAEKREHEKEVL
          ASGQAFELI..P...K...P..P...PKK.DLSLEEIQKKLEAAEERR.SHEAEVLKQLAE.RE.EKEV.
Retrocopy ASGQAFELIFTPLHQKNLSPISPFPTPKKEDLSLEEIQKKLEAAEERRTSHEAEVLKQLAETREREKEVP

Parental  QKAIEENNNFSKMAEEKLTH-KMEANKENREAQ-MAAKLERLREKDKHVEEVRKNKESKDPAD-ETEAD
          QKA.E.NNNFSKMA.EK.TH.K.EAN.ENRE.Q.MAA.LERLREKDK.VEEVRKN..SKDPA..E.EAD
Retrocopy QKATEKNNNFSKMAKEKRTH>KIEANEENREVQ<MAAELERLREKDKRVEEVRKNEDSKDPAE<EPEAD

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	331.66 RPM
SRP017611_kidney	0.00 RPM	46.20 RPM
SRP017611_liver	0.00 RPM	1.95 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1855 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1855 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1855 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206, retro_cjac_474,
Equus caballus	ENSECAG00000021662	1 retrocopy	retro_ecab_490,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mustela putorius furo	ENSMPUG00000015774	1 retrocopy	retro_mputfur_1191,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Pteropus vampyrus	ENSPVAG00000006344	1 retrocopy	retro_pvam_53,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855 , retro_rnor_2048, retro_rnor_765,
Sorex araneus	ENSSARG00000011057	2 retrocopies	retro_sara_271, retro_sara_764,
Sarcophilus harrisii	ENSSHAG00000006382	1 retrocopy	retro_shar_391,