RetrogeneDB ID: retro_rnor_2953

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:92253808..92255292(-)
• 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_2953
ATGGGAGGTCTGGAGAAGAAGTATGAACGAGGCTTTGCCACAGATTGTATCACCGGAAACAAAGCCCAGAAGAAGCTGCA
GCTGAACCTATCTGATTTCAGGCTGCTGTGCAGCCTTAAAGGTATTTATGCTCAAGAACCAAAGCATAAGAAGAAAGTTA
ACAAGCGTTCCACAGCAGCCCAAACATTTTACCTTATCAAAGATAGTAAATTCCTCCTCCATGACCCTATCATCAATAAG
CTCCGAGAGTACAAGGTATTTATCTGGAAGCTCCACAAAGCCTATGGGAAAAGAAAATGGAATCCTGTGGAGCACCTGAA
GGACAATAAACACACTTACAAAATTTACCATATTGTCAAGGAGTGATACCCCACGTTTATTGATGCGTTGGAGGACCTCA
ATTATGCCCTGTTATTTTTCTTCCATTTCTCCACATTCCCTGAGACAGGCAAGTGCCATATGCAGACCAATCAGCTGTAC
TGCTGATTCACTGTGGAGTTTCTGCACTAAGTCATCGCTGTCCTAGCCCTGAGCAAGTCCACTGAAGGCACTTACTATCA
GGATGAGGTGCTGGGTCAGCCCATCAAACGGATTTAACCCTACGCTTTCTCCCATGATCATACAATAGATGTGGACTACT
GAGTCATGGCCACCTTCACAGTGTTCTGTACCACTCTCCTGGGCTTCTGCCTCTACCAATTACTCAACCTTCATTACTCA
CCCAAGCTTGAAGTTCAAGCTCAATCAGAGACAAAAGTCAGCGTAGACCCATATGCATTGAACTCTGAGAACTCTACGGA
GAAACTGGCTGCACTCAGTGCCAGCCTTGGCCGAGTGGTGGTGCCTGCTATAGAGGAGGCTGAGGCGATGTGTTTCCTAC
TGACCAAGGAGGTGATAGCAAAGGAGGAAGGTCAAAGGAAAGAGCTGGAGGCACAGGAAAAGCACAAGAAACTCTTTGAA
GGCCTGAAGTTCTTCCTGAACTGAGACGTACACCATGAAGCATTGGCCTTCCTCTTCAGGAGTGTTGGTGGAGATGTATC
CTGGGACAAGCCTTTGCGCATCGGTGCCACCTATGACATCACAGACTCTTGCATCACCCACTAGATTGTTGATCAGCCGC
CGGGACAGCAATCCCCATTCATTAGCAGGTACTATATACAGCCCCAGTGGGTGATTGACTATGTGAATGCCCAGCTCCTC
CTCCCTGTGGCAGAGTACTTCCCTGGGGTTGCACTTGTCCCCACACCTTTTTCCCTTTGTATTGAGAACGAAGGAGATTA
TATTCCTTCTGAGAAGCTGAAGCTCCTGGCTCTGTAGCAAGGAGAAAACCCAGGAAGAAGAAGAGGAAGACAAGGTTGAT
GAAGACAATTACAACAAAGGCAGCAGAAAACGAGAAGAAATATGTAGAAGCTGAATCAGAGGAGGAAGAGGAGGCACATC
TGTCGGCCTTGGAGCAGCAAAGGATGGAAAGAAGGAAGCCTCAG

Alignment

ORF - retro_rnor_2953 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.64 %
• Parental protein coverage: 85.32 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MGGLEKKKYERGSATNYITRNKARKKLQLSLPDFRRLCILKGIYPHEPKHKKKVNKGSTAARTFYLIKDI
          MGGLEKK.YERG.AT..IT.NKA.KKLQL.L.DFR.LC.LKGIY..EPKHKKKVNK.STAA.TFYLIKD.
Retrocopy MGGLEKK-YERGFATDCITGNKAQKKLQLNLSDFRLLCSLKGIYAQEPKHKKKVNKRSTAAQTFYLIKDS

Parental  KFLLHEPIVNKFREYKVFVRKLRKAYGKSEWNAVERLKDNKPSYKLDHIVKERYPTFIDALRDLDDALSM
          KFLLH.PI.NK.REYKVF..KL.KAYGK..WN.VE.LKDNK..YK..HIVKE.YPTFIDAL.DL..AL..
Retrocopy KFLLHDPIINKLREYKVFIWKLHKAYGKRKWNPVEHLKDNKHTYKIYHIVKE*YPTFIDALEDLNYALLF

Parental  CFLFSTFPRTGKCHVQTIQLCRRLTVEFMHYVIAARALRKVFLSIKGIYYQAEVLGQPIVWIAPYAFSHD
          .F.FSTFP.TGKCH.QT.QL....TVEF.H.VIA..AL.K...S..G.YYQ.EVLGQPI..I.PYAFSHD
Retrocopy FFHFSTFPETGKCHMQTNQLYC*FTVEFLH*VIAVLALSK---STEGTYYQDEVLGQPIKRI*PYAFSHD

Parental  HPTDVDYRVMATFTEFYTTLLGFVNFRLYQSLNLHYPPKIESQAQAEMKVSEDTYALDSESSMEKLAALS
          H..DVDY.VMATFT.F.TTLLGF....LYQ.LNLHY.PK.E.QAQ.E.KVS.D.YAL.SE.S.EKLAALS
Retrocopy HTIDVDY*VMATFTVFCTTLLGFC---LYQLLNLHYSPKLEVQAQSETKVSVDPYALNSENSTEKLAALS

Parental  ASLARVVVPAVEEAEA-DEFPTD-GEVTAQEEDRRKELEAQEKHKKLFEGLKFFLNREVPREALAFIIRS
          ASL.RVVVPA.EEAEA.D.FPTD..EV.A.EE..RKELEAQEKHKKLFEGLKFFLN..V..EALAF..RS
Retrocopy ASLGRVVVPAIEEAEA<DVFPTD>KEVIAKEEGQRKELEAQEKHKKLFEGLKFFLN*DVHHEALAFLFRS

Parental  FGGDVSWDKSLCIGATYDSTDSGITHQIVDR-PGQQTPIIGRYYVQPQWVFDCVNARLLLPVAEYFPGV-
          .GGDVSWDK.L.IGATYD.TDS.ITH.IVD..PGQQ.P.I.RYY.QPQWV.D.VNA.LLLPVAEYFPGV.
Retrocopy VGGDVSWDKPLRIGATYDITDSCITH*IVDQPPGQQSPFISRYYIQPQWVIDYVNAQLLLPVAEYFPGV>

Parental  QLPPHLSPFV-SEKEGDYIPPEKLKLLALQRGEDPGNL-EEEEEDEDDEGDDS-EGDGDVAVENEEEVVE
          .L.PHL.PFV..E.EGDYIP.EKLKLLAL..GE.PG...EE...DED.....S.E..........EE..E
Retrocopy HLSPHLFPFV<IENEGDYIPSEKLKLLAL*QGENPGRR>EEDKVDEDNYNKGS>ENEKKYVEAESEEEEE

Parental  AESEEEEEAHLSALEQQ
          A.....E.........Q
Retrocopy AHLSALEQQRMERRKPQ

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_2953 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2953 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2953 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,