RetrogeneDB ID: retro_rnor_1638

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:133195239..133196115(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdk1
• Ensembl ID: ENSRNOG00000000632
• Aliases: Cdk1, Cdc2, Cdc2a
• Description: Cyclin-dependent kinase 1 [Source:UniProtKB/Swiss-Prot;Acc:P39951]

Sequence

>retro_rnor_1638
GTGGAAGACTATATTAAAACAGAGAAAAGTGGGGAAGGGACTTACGGTGTGGTATATGAGGGTAGACACAGAACTACTGG
CCAGACAGTGGCCATGAAGAAAATCAGACTTGAAAGCAAGGAAGAAGGAGGGCCCAGTACTGCAATCCGGGAAGTCTCTC
TATTAAAAGAACTCTGACATCCAAATATAGTCAGCCTGCAGGGTGTGCTCATGCAGGACTCCGGCTGTATCTCATCTTTG
AGTTCCTGTCCATGGACCTCAAGAAGCACCTGGACTTTATCCCTCCTGGCCACTTCATGGATTCTTGACTCCTTAAGAGT
TACTTGTACCAAATCCTCCAGGGGACTGTGTTTTGTCACTCCAGACAAATTCTTCACAGAGACTTGAAACCTCAAAATCT
ATTGATTGATGACAAAGGAACTATCAAACTGGCTGATTCTGGCCTTTCCAGGGCATTTGGAATACCGATAAGAGTGTACA
CAAATGAGGTGGTGGCCCTGTGGTACCGATCTCCAGACGTGTTGCTGGGCTCCACTTGCTACTCCACCCCACTTGACATC
TGGAGCATAGGGACCATATTTGCAGAGCTGCCAACCAAGAAGCCACTTTTCCATGGTGATTCAGAGACTGACTAGCTCTT
CGGAATTTTCAGAGGTCTGGGTACCCCTAACAACAAAGGGTGGCCAGAAGTAGAGCCCCTGCAGGACTACAAGAGCACTT
TTCCCAAATGGAAGCCAGGGAGCCTCGCATATCAAGGACCGGGATGACGGCTTGGCTTTTCTCTCAAAGATGCTAGTCTA
TGATCCTGCCTAATAAATGTCTGGGAAAACGGCCCTCAGGCACCCATCCTTTGATAACCTGGGCAATCAGGTTAAG

Alignment

ORF - retro_rnor_1638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEDYIKIEKIGEGTYGVVYKGRHRTTGQIVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVL
          .EDYIK.EK.GEGTYGVVY.GRHRTTGQ.VAMKKIRLES.EEG.PSTAIRE.SLLKEL.HPNIVSLQ.VL
Retrocopy VEDYIKTEKSGEGTYGVVYEGRHRTTGQTVAMKKIRLESKEEGGPSTAIREVSLLKEL*HPNIVSLQGVL

Parental  MQDS-RLYLIFEFLSMDLKKYLDSIPPGQFMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDK
          MQDS.RLYLIFEFLSMDLKK.LD.IPPG.FMDS.L.KSYLYQILQG.VFCHSR..LHRDLKPQNLLIDDK
Retrocopy MQDS<RLYLIFEFLSMDLKKHLDFIPPGHFMDS*LLKSYLYQILQGTVFCHSRQILHRDLKPQNLLIDDK

Parental  GTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSE
          GTIKLAD.GL.RAFGIPIRVYT.EVV.LWYRSP.VLLGS..YSTP.DIWSIGTIFAEL.TKKPLFHGDSE
Retrocopy GTIKLADSGLSRAFGIPIRVYTNEVVALWYRSPDVLLGSTCYSTPLDIWSIGTIFAELPTKKPLFHGDSE

Parental  IDQLFRIFRALGTPNNEVWPEVESLQDYKNTF-PKWKPGSLASHVKNLDENGLDLLSKMLVYDPAKRISG
          .D.LF.IFR.LGTPNN..WPEVE.LQDYK.TF.P....G..ASH.K..D..GL..LSKMLVYDPA...SG
Retrocopy TD*LFGIFRGLGTPNNKGWPEVEPLQDYKSTF>PNGSQG--ASHIKDRDD-GLAFLSKMLVYDPA**MSG

Parental  KMALKHPYFDDLDNQIK
          K.AL.HP.FD.L.NQ.K
Retrocopy KTALRHPSFDNLGNQVK

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	0.93 RPM
SRP017611_kidney	0.00 RPM	1.12 RPM
SRP017611_liver	0.00 RPM	0.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1638 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1638 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Cavia porcellus	ENSCPOG00000005402	3 retrocopies	retro_cpor_1414, retro_cpor_1422, retro_cpor_200,
Dasypus novemcinctus	ENSDNOG00000018590	1 retrocopy	retro_dnov_265,
Equus caballus	ENSECAG00000009716	1 retrocopy	retro_ecab_637,
Felis catus	ENSFCAG00000014972	1 retrocopy	retro_fcat_329,
Microcebus murinus	ENSMICG00000005793	1 retrocopy	retro_mmur_43,
Monodelphis domestica	ENSMODG00000017091	1 retrocopy	retro_mdom_702,
Rattus norvegicus	ENSRNOG00000000632	1 retrocopy	retro_rnor_1638 ,
Tupaia belangeri	ENSTBEG00000017549	3 retrocopies	retro_tbel_3309, retro_tbel_807, retro_tbel_812,
Tursiops truncatus	ENSTTRG00000001085	2 retrocopies	retro_ttru_1619, retro_ttru_1634,