RetrogeneDB ID: retro_cpor_200

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_10:16573238..16574129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK1
• Ensembl ID: ENSCPOG00000005402
• Aliases: None
• Description: None

Sequence

>retro_cpor_200
ATGGAAGACTACACTAAAATAGAGAAAATTGGAGAAGGTACTTACGGAGTTGTATATAAGGGTAGACACAAAACTACAGG
TCAAGTAGTAGCCATGAAGAAAATCAGACTAGAAAGTGAAGAGGAAGGGGTTCCTAGTACTGCAATTCGGGAAATTTCTC
TATTAAAAGAACTTCGTCATCCAAATATAGTCAGTCTTCAAGATGTGATTATGCAAGATTCCAGGTTATATCTCATTTTT
GAATTCCTTTCAATGGATCTCAAGAAATACTTGGATTCTATTCCTGCTGGGTAGTTCATGGATTCACCACTTGTTAAGAG
TTATTTGTACCAGATCCTTCAGGGTATTGTATTTTGTCACTCTAGAAGAGTTCTTCACAGAGACTTAAAACCTCAAAATC
TGTTGATTGATGACAAAGGAACAGTTAAACTGGCTGACTTTGGCCTTGCTAGAGCTTTTGGGATACCTATTAGAGTATAT
ACACATGAGGTAGTAACACTCTGGTATAGATCTCCAGAAGTATTGATGGGGTCAGCTCAGTACTCTACTCCAGTAGACAT
TTGGAGTATAGGCACAATCTTTGCAGAATTGGCAACTAAGAAACCACTTTTCCATGGGGATTCAGAAATTGATCAACTGT
TCAGGATTTTCAGAGCTTTAGGCACTCCCAACAATGAAGTATGGCCAGAAGTGGAATCTTTACAGGACTATAAGAATACA
TTTCCCAAGTGGAAACCAGGAAGCCTAGCATCCCATGTCAAAAACTTGGATGAAAATGGCTTGGATTTACTCTCGAAAAT
GTTAGCCTATGATCCTGCTAAACGAATTTCTGGCAAAATGGCACTGAATCATCCATATTTTAATGATTTGGACAATCAGA
TTAAGAAGATG

Alignment

ORF - retro_cpor_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.56 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVL
          MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDV.
Retrocopy MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVI

Parental  MQDSRLYLIFEFLSMDLKKYLDSIPAGQFMDSSLVKASYANEILY--IHMHKLALFDLCLLLITFLIYVK
          MQDSRLYLIFEFLSMDLKKYLDSIPAG.FMDS.LVK.SY...IL......H........L.....LI..K
Retrocopy MQDSRLYLIFEFLSMDLKKYLDSIPAG*FMDSPLVK-SYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDK

Parental  NALSDLDFLLLLIFGMQEKNSSYEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSE
          ......DF.L...FG........EVVTLWYRSPEVL.GSA.YSTPVDIWSIGTIFAELATKKPLFHGDSE
Retrocopy GTVKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLMGSAQYSTPVDIWSIGTIFAELATKKPLFHGDSE

Parental  IDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLVYDPAKRISGK
          IDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKML.YDPAKRISGK
Retrocopy IDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLAYDPAKRISGK

Parental  MALNHPYFNDLDNQIKKM
          MALNHPYFNDLDNQIKKM
Retrocopy MALNHPYFNDLDNQIKKM

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	0.12 RPM	0.35 RPM
SRP017611_kidney	0.21 RPM	1.36 RPM
SRP017611_liver	0.44 RPM	0.96 RPM
SRP040447_lung	1.16 RPM	4.16 RPM
SRP040447_skeletal_muscle	0.16 RPM	0.30 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_200 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_200 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007001	2 retrocopies	retro_cjac_1846, retro_cjac_671,
Cavia porcellus	ENSCPOG00000002670	1 retrocopy	retro_cpor_457,
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,