RetrogeneDB ID: retro_rnor_824

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:25367413..25368539(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pes1
• Ensembl ID: ENSRNOG00000004515
• Aliases: None
• Description: Pescadillo homolog [Source:UniProtKB/Swiss-Prot;Acc:Q3B8N8]

Sequence

>retro_rnor_824
ACCCATGATAATACAACAGATGTGGACTAAAGAGTCATGGCCACCTTCACTGAGTTCTATACCACTCTCCTGGGCTTCAT
CAACTTCCGCCTCTACTAGTCACTCACACTTCACTATCCCCCCAAGATTGAAGGTCAAGCCCAAGTAGAAACTAAAGTTA
GTAAGGACACATATGCATTGGACTCTGACAGCTCTATGGAGAAACTGACTGCCCTCAGTGCCAGCCTGGCCCGAGTGGTG
GTGCCTGCTATACAGGAGGCTGAGGCTGATGGGTTTCCTACTGGCAGGGAGGTGAAAGCACAGGAGAAAGGTTGAAGGAA
AGAGCTGGAAGCACAGGAAAAGCCCAAGAAACTCTTTGAAGCCTGAAGTTCTTCCCGAACCAAGAGGTTCCCAGTGAAGC
GTTGGCTTTCATCATCAGGAGTTTTGGTAGGGATGTATCCTGGGACAAGTCTTTGTGCGTTGGAGCCATCTATGACAACA
CAGACTCTTGCATCACCTGCCAGATTGTTGAGCGGCCAAGGCAGCAAACCCCCATCATTGCCAGGTACTGCGTACAGCCC
CAGTGGGTGTTTGACTGTCTGAATGCCAGGCTCCTCCTCCCTGTGGCAGAATATTTCCCTGGGGTGCAGCTGCCCCCAAA
CCTTTTACCCTTCATAGCTGAGAAGGAAGGAGATTACATTCCCTCTGAGAAGCTGAAGCTCCTGGTTCTGCAGCAGGGAG
AAGACCCAGGAAACTTGGAAGAGGAAGACGAGGATGATGAAGACAATGACAATGAAGGTGACACTGGTGTTGCAGCAGAA
AACAAAGAGGAAGATGTGGAAGCTGAATCAGAGGAGGAGAAGGAGGCGCACCTGTCAGCCTTGGAGCAGCAAAGCTGGAA
GGAAAGAAGCCCCAGGTTAAGGCCTGCACCGTGAAGCTGAAAGACAAGCAGCCACTGGCCCCGGAGGAAGAGACTGAGGC
CAACCATCTGGCCATCATGATGAAGAAGCGAGAGAAGGACCTTTAACAAAAGATCATGTTCTGCAAGCGGCACAAAATCT
GAGAGGCCAACAAGCTCCCAGAGAAGAGGAAAGCACATGAGGACACTTTGAAGTCTGAGGAAGAAGTCAAGAGGACAAGG
CCTGTG

Alignment

ORF - retro_rnor_824 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 64.68 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHDHPTDVDYRVMATFTEFYTTLLGFVNFRLYQSLNLHYPPKIESQAQAEMKVSEDTYALDSESSMEKLA
          .HD..TDVD.RVMATFTEFYTTLLGF.NFRLY.SL.LHYPPKIE.QAQ.E.KVS.DTYALDS.SSMEKL.
Retrocopy THDNTTDVD*RVMATFTEFYTTLLGFINFRLY*SLTLHYPPKIEGQAQVETKVSKDTYALDSDSSMEKLT

Parental  ALSASLARVVVPAVEEAEADEFPTDGEVTAQEEDRRKELEAQEKHKKLFEG-LKFFLNREVPREALAFII
          ALSASLARVVVPA..EAEAD.FPT..EV.AQE...RKELEAQEK.KKLFE..LKFF.N.EVP.EALAFII
Retrocopy ALSASLARVVVPAIQEAEADGFPTGREVKAQEKG*RKELEAQEKPKKLFEA<LKFFPNQEVPSEALAFII

Parental  RSFGGDVSWDKSLCIGATYDSTDSGITHQIVDRPGQQTPIIGRYYVQPQWVFDCVNARLLLPVAEYFPGV
          RSFG.DVSWDKSLC.GA.YD.TDS.IT.QIV.RP.QQTPII.RY.VQPQWVFDC.NARLLLPVAEYFPGV
Retrocopy RSFGRDVSWDKSLCVGAIYDNTDSCITCQIVERPRQQTPIIARYCVQPQWVFDCLNARLLLPVAEYFPGV

Parental  QLPPHLSPFVSEKEGDYIPPEKLKLLALQRGEDPGNLEEEEEDEDDEGDDSEGDGDVAVENEEEVVEAES
          QLPP.L.PF..EKEGDYIP.EKLKLL.LQ.GEDPGNL..EEEDEDDE..D.EGD..VA.EN.EE.VEAES
Retrocopy QLPPNLLPFIAEKEGDYIPSEKLKLLVLQQGEDPGNL--EEEDEDDEDNDNEGDTGVAAENKEEDVEAES

Parental  EEEEEAHLSALEQQ-RLGGKKPQVMAGTVKLEDRQRLAQEEESEAKRLAIMMMKKREKYLYQKIMFGKRR
          EEE.EAHLSALEQQ..L.GKKPQV.A.TVKL.D.Q.LA.EEE.EA..LAI.MMKKREK.L.QKIMF.KR.
Retrocopy EEEKEAHLSALEQQ<KLEGKKPQVKACTVKLKDKQPLAPEEETEANHLAI-MMKKREKDL*QKIMFCKRH

Parental  KIREANKLAEKRKAHDDAVRSEKKAKRTRPV
          KI.EANKL.EKRKAH.D...SE...KRTRPV
Retrocopy KI*EANKLPEKRKAHEDTLKSEEEVKRTRPV

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	36.02 RPM
SRP017611_kidney	0.00 RPM	37.33 RPM
SRP017611_liver	0.00 RPM	23.40 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_824 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_824 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_824 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010617	1 retrocopy	retro_cjac_3182,
Cavia porcellus	ENSCPOG00000003565	1 retrocopy	retro_cpor_986,
Homo sapiens	ENSG00000100029	1 retrocopy	retro_hsap_4133,
Mus musculus	ENSMUSG00000020430	2 retrocopies	retro_mmus_1393, retro_mmus_3225,
Otolemur garnettii	ENSOGAG00000005804	1 retrocopy	retro_ogar_1719,
Pongo abelii	ENSPPYG00000011716	1 retrocopy	retro_pabe_3471,
Pan troglodytes	ENSPTRG00000014251	2 retrocopies	retro_ptro_2018, retro_ptro_2809,
Rattus norvegicus	ENSRNOG00000004515	2 retrocopies	retro_rnor_2953, retro_rnor_824 ,
Tupaia belangeri	ENSTBEG00000009825	1 retrocopy	retro_tbel_1000,