RetrogeneDB ID: retro_cjac_2633

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:87801289..87802621(-)
• Located in intron of: ENSCJAG00000015336

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK6
• Ensembl ID: ENSCJAG00000000962
• Aliases: None
• Description: None

Sequence

>retro_cjac_2633
TCAGATCTTTTCATTAATACTGAAGACTTGGTGCTGTAGATAGGTGACTTTGGTCTTGCACAGATCATAGATCCTCATTA
TTCCCATAAGGGTCATCTTTCTGAAGGATTGGTTACTAAATGCTACAGATCATCACATCTTTTACTTTCTCCTAATAATT
ACATGAAAGCCATGACATGTGGGCAGTAGGCTGCATCTTTGCTGAAATGCTGACTGGTAAAACCCTTTTTGCAGATGCAA
ATGAACTTGAACAGATGCAGCTGATTTTAGAATCTATTTCTGTTGTACATGAGGAAGATCGTCAGGAGCTTCTCAGCGTA
ATTCCAGTTTACATTAGAAATGACATGACTGAATCACACAAACCTTTAACTCAGCTGCTTCCAGGAATTAGTAGAGAAGC
ACTGGATTTCCTGGAACAAATTTTGACATTTAGCCCCAAGGATCAGTTAACAGCAGAAGCAGCGCTCTCCCATCCTTCAT
GAGCATATATTCTTTTCCAATGAATGAGCCAATTTCAAGCCATCCTTTTCATATTGAAGATGAAGTTGATGATATTTTGC
TTATGGATGAAACTCACAGTCACATTAATAACTGGGAAAGGTACCATGATTGTCAGTTTTCAGGGCATGATTGGCCTATA
CATAACAACTTTGATATTGATGAAGTTGAGCTTGATCCAAGAGCTCTGTCTGATGTCACTGATGAAGAGGAAGTACAAGT
TGATCCCCGAAAATATTTGGATGGAGATGGGGAAAAGTATCTGGAAGATCCTGCTTTTGATACCAGTTACTCTACTAAGC
CTTGTTGGCAGTACCCAGATCATCATTAAAACAAATACTGTGATCTGGAGTGTAGCCATACTTGTAACTACAAAACTATG
TCATCATCATATTTAGATACTTTTGTTTGCAGAGAGAGTGAAGTTAACCATTACTATGAGCCCAAGCTTATTATAGATAT
TTACAAATGGAAAGAACAAAGCAAAGAAAAATCTGATAAGAAAGGCAAATCAAAATGTGAAAGGAATGGATTGGTTAAAG
CCCAGATAGCACTGGAGGAAGCATCACAGCAACTGGCCAGAAAAGGGAAAAGAATCAGGGATTTGATTTTGATTCCTTTA
TTGCAGGAACTATTCAACTTAGTTCCCAACATGAGCCTACTGATGTTGTTGATAAATTAAATGACTTGAATAGCTCAGTG
TCCCAACTAGAGTTGAAAAGTTTGATATCAAAGTCAGTAAGCCAAGAAAAACAGGAAAAAGGAATGGCAAATTTGGCTCA
ATTGGAAGACTTATACCAATCTTCTTGGGACAGTTTGTGAGTGGTGGGGAGG

Alignment

ORF - retro_cjac_2633 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.09 %
• Parental protein coverage: 61.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYTKAI-DMWAAGCIFAE
          ..LFINTEDLVL.IGDFGLA.I.DPHYSHKGHLSEGLVTK.YRS..LLLSPNNY.KA..DMWA.GCIFAE
Retrocopy SDLFINTEDLVL*IGDFGLAQIIDPHYSHKGHLSEGLVTKCYRSSHLLLSPNNYMKAM<DMWAVGCIFAE

Parental  MLTGKTLFAGAHELEQMQLILESIPVVHEEDRQELLSVIPVYIRNDMTEPHKPLTQLLPGISREALDFLE
          MLTGKTLFA.A.ELEQMQLILESI.VVHEEDRQELLSVIPVYIRNDMTE.HKPLTQLLPGISREALDFLE
Retrocopy MLTGKTLFADANELEQMQLILESISVVHEEDRQELLSVIPVYIRNDMTESHKPLTQLLPGISREALDFLE

Parental  QILTFSPMDRLTAEEALSHP-YMSIYSFPMDEPISSHPFHIEDEVDDILLMDETHSHIYNWERYHDCQFS
          QILTFSP.D.LTAE.ALSHP..MSIYSFPM.EPISSHPFHIEDEVDDILLMDETHSHI.NWERYHDCQFS
Retrocopy QILTFSPKDQLTAEAALSHP<FMSIYSFPMNEPISSHPFHIEDEVDDILLMDETHSHINNWERYHDCQFS

Parental  EHDWPIHNNFDIDEVQLDPRALSDVTDEEEVQVDPRKYLDGDREKYLEDPAFDTNYSTEPCWQYPDHHEN
          .HDWPIHNNFDIDEV.LDPRALSDVTDEEEVQVDPRKYLDGD.EKYLEDPAFDT.YST.PCWQYPDHH.N
Retrocopy GHDWPIHNNFDIDEVELDPRALSDVTDEEEVQVDPRKYLDGDGEKYLEDPAFDTSYSTKPCWQYPDHH*N

Parental  KYCDLECSHTCNYKTRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEKSDKKGKSKCERNGLVKA
          KYCDLECSHTCNYKT.SSSYLD..V.RESEVNHYYEPKLIID...WKEQSKEKSDKKGKSKCERNGLVKA
Retrocopy KYCDLECSHTCNYKTMSSSYLDTFVCRESEVNHYYEPKLIIDIYKWKEQSKEKSDKKGKSKCERNGLVKA

Parental  QIALEEASQQ-LAGKEREKNQGFDFDSFIAGTIQLSSQHEPTDVVDKLNDLNSSVSQLELKSLISKSVSQ
          QIAL.E...Q...G..REKNQGFDFDSFIAGTIQLSSQHEPTDVVDKLNDLNSSVSQLELKSLISKSVSQ
Retrocopy QIAL-EEASQ<ATGQKREKNQGFDFDSFIAGTIQLSSQHEPTDVVDKLNDLNSSVSQLELKSLISKSVSQ

Parental  EKQEKGMANLAQLEALYQSSWDSQFVSGR
          EKQEKGMANLAQLE.LYQSSWDS..V.GR
Retrocopy EKQEKGMANLAQLEDLYQSSWDSL*VVGR

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
SRP051959_colon	0.13 RPM	54.27 RPM
SRP051959_heart	0.51 RPM	17.66 RPM
SRP051959_kidney	0.18 RPM	27.95 RPM
SRP051959_liver	0.02 RPM	22.53 RPM
SRP051959_lung	0.11 RPM	19.26 RPM
SRP051959_lymph_node	0.07 RPM	18.81 RPM
SRP051959_skeletal_muscle	0.28 RPM	15.24 RPM
SRP051959_spleen	0.06 RPM	24.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2633 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2633 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2633 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633 ,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441, retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879, retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75,