RetrogeneDB ID: retro_cjac_2740

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:79560573..79562221(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034296
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ME1
• Ensembl ID: ENSCJAG00000009064
• Aliases: None
• Description: Malic enzyme [Source:UniProtKB/TrEMBL;Acc:F6Y1T8]

Sequence

>retro_cjac_2740
CTTGATTCTGACTTGGCCTTTACCCTGGAAGAGAGACAGCAATTGAACATTCATGGATTGTTGCCACCTTCCTTCATCAG
TCAGGAGATTCAGGTCCTTAGAGTACTAATAAATTTTGAGCGTCTGAAGTCTGACTTTGACAGGTATCTTCTCTTAATGG
ATCTCCAAGGTAGAAATGAAAAACTCTTTTATCGAGTGCTAACATCTGACATTGAGAAATTCATGCCTATTGTTTATACT
CCCACTGTGGGTCTGGCTTGCCAACGATATAGTTTAGTGTTTCGAAAGCCAAGAGGTCTCTTTATTAGTATCCATGATTG
TGGGCATATTGCTTCAGTTCTCAATGCATGGCCAGAAGATGTCATCAAGGCCATTGTGATGACCGATGGAGAGTGTATTC
TTGGCTTGGGAGATCTTGGCTGTAATGGAATGGGCATCCCTGTGGGTAAATTGGCTCTATATACAGCTTGTGGAGGGATG
AATCCTCAAGAATGTCTGCCTGTCATTCTGGATGTGGGAACTGAAAATGAGGAGTTACTTAAAGATCCACTCTACGTTGG
ACTACGGCAGAGAAGAGTAAGAGGTTCTGAATATGATGATTTTTTTGGATGAATTCATGGAGGCAGTTTCTTCCAAGTAT
GGCATGAATTGCCTTACTCAGTTTGAAGATTTTGCCAACGTGAATGCACTTCGTCTCCCGAACAAGTATCGAAACCACTA
TTGCACATTCAATGATGATATTCAAGAAACAGCGTCTGTTGCAGTAGCAGGTCTCCTTGCAGCTCTTGGAATAACCAAGA
ACAAACTGTCTGATCAAACAATACTATTCCAAGGAGCTGGAGAGGCTGCCTTAGGGATTGCACACCTGATTGTGATGGCA
ATGGAAAAAGAAGGTTTACCAAAAGAGAAACCCATCAAAAAGATATGGTTGGTTGATTCAAAAGGATTAATAGTTAAGGG
ACGTGCTTCCTTAACACAAGAGAAAGAGAAATTTGCCCATGAACATGAAGAAATGAAGAATCTAGAAACCATTGTTCAAG
AAATAAAACCAACTGCCCTCATAGGAGTTGCTGCAATTGGTGGTGCATTCTCAGAACAAATTCTCAAAGATATGGCTGCC
TTCAATGAACGGCCTATTATTTTTGCTTTGAGTAATCCAACTAGCAAAGCAGAATGTTCTGCAGAGCAGTGCTATAAAAT
AACCAAGGGACGTGCAATTTTTGCCAGTGGCAGTCCTTTTGATCCAGTCAGTCTACCAAATGGACAGACCCTATATCCTG
GGCAAGGCAACAATTCCTATGTGTTCCCTGGAGTTGCTCTTGGTGTTGTGGCGTGTGGATTGAAGCACATCACAGATAAT
GTTTTCCTCACTACTGCTGAGGTTATAGCTCAGCAAGTGTCAGATAAACACTTGGAAGAGGGTTAGCTTTATCCTCCTTT
GAATACCATTAGAGATATTTCTCTGAAAATTGCAGAAAAGATTGTGAAAGATGCATACCAAGAAAAGACAGCCACAGTTT
ATCCTGAACTGCAAAACAAAGAAGCATTTATCCGCTCCCAGATGTATAGTACTGATTATGACCAGATTCTACCTGATTGT
TATTCTTGGCCTGAAGAGGTCCAGAAAATACAGACCAAAGTTGACCAG

Alignment

ORF - retro_cjac_2740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.64 %
• Parental protein coverage: 95.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNKDLAFTLEERQQLNIHGLLPPSFISQEIQVLRVLKNFERLKSDFDRYLLLMDLQDRNEKLFYRVLTSD
          L..DLAFTLEERQQLNIHGLLPPSFISQEIQVLRVL.NFERLKSDFDRYLLLMDLQ.RNEKLFYRVLTSD
Retrocopy LDSDLAFTLEERQQLNIHGLLPPSFISQEIQVLRVLINFERLKSDFDRYLLLMDLQGRNEKLFYRVLTSD

Parental  IEKFMPIVYTPTVGLACQQYSLVFRKPRGLFISIHDRGHIASVLNAWPEDVIKAIVVTDGERILGLGDLG
          IEKFMPIVYTPTVGLACQ.YSLVFRKPRGLFISIHD.GHIASVLNAWPEDVIKAIV.TDGE.ILGLGDLG
Retrocopy IEKFMPIVYTPTVGLACQRYSLVFRKPRGLFISIHDCGHIASVLNAWPEDVIKAIVMTDGECILGLGDLG

Parental  CNGMGIPVGKLALYTACGGMNPQECLPVILDVGTENEELLKDPLYIGLRQRRVRGSEYDDF-LDEFMEAV
          CNGMGIPVGKLALYTACGGMNPQECLPVILDVGTENEELLKDPLY.GLRQRRVRGSEYDDF.LDEFMEAV
Retrocopy CNGMGIPVGKLALYTACGGMNPQECLPVILDVGTENEELLKDPLYVGLRQRRVRGSEYDDF>LDEFMEAV

Parental  SSKYGMNCLIQFEDFANMNAFRLLNKYRNHYCTFNDDIQGTASVAVAGLLAALRITKNKLSDQTILFQGA
          SSKYGMNCL.QFEDFAN.NA.RL.NKYRNHYCTFNDDIQ.TASVAVAGLLAAL.ITKNKLSDQTILFQGA
Retrocopy SSKYGMNCLTQFEDFANVNALRLPNKYRNHYCTFNDDIQETASVAVAGLLAALGITKNKLSDQTILFQGA

Parental  GEAALGIAHLIVMAMEKEGLPKEKAIKKIWLVDSKGLIVKGRASLTQEKEKFAHEHEEMKNLETIVQEIK
          GEAALGIAHLIVMAMEKEGLPKEK.IKKIWLVDSKGLIVKGRASLTQEKEKFAHEHEEMKNLETIVQEIK
Retrocopy GEAALGIAHLIVMAMEKEGLPKEKPIKKIWLVDSKGLIVKGRASLTQEKEKFAHEHEEMKNLETIVQEIK

Parental  PTALIGVAAIGGAFSEQILKDMAAFNERPIIFALSNPTSKAECSAEQCYKITKGRAIFASGSPFDPVTLP
          PTALIGVAAIGGAFSEQILKDMAAFNERPIIFALSNPTSKAECSAEQCYKITKGRAIFASGSPFDPV.LP
Retrocopy PTALIGVAAIGGAFSEQILKDMAAFNERPIIFALSNPTSKAECSAEQCYKITKGRAIFASGSPFDPVSLP

Parental  NGQTLYPGQGNNSYVFPGVALGVVACGLKHITDKVFLTTAEVIAQQVSDKHLEEGRLYPPLNTIRDVSLK
          NGQTLYPGQGNNSYVFPGVALGVVACGLKHITD.VFLTTAEVIAQQVSDKHLEEG.LYPPLNTIRD.SLK
Retrocopy NGQTLYPGQGNNSYVFPGVALGVVACGLKHITDNVFLTTAEVIAQQVSDKHLEEG*LYPPLNTIRDISLK

Parental  IAEKIVKDAYQEKTATVYPEPQNKEAFILSQMYSTDYDQILPDCYSWPEEVQKIQTKADQ
          IAEKIVKDAYQEKTATVYPE.QNKEAFI.SQMYSTDYDQILPDCYSWPEEVQKIQTK.DQ
Retrocopy IAEKIVKDAYQEKTATVYPELQNKEAFIRSQMYSTDYDQILPDCYSWPEEVQKIQTKVDQ

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	0.02 RPM	14.31 RPM
SRP051959_heart	0.02 RPM	18.14 RPM
SRP051959_kidney	0.02 RPM	5.17 RPM
SRP051959_liver	0.00 RPM	15.40 RPM
SRP051959_lung	0.03 RPM	3.30 RPM
SRP051959_lymph_node	0.00 RPM	1.30 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.71 RPM
SRP051959_spleen	0.02 RPM	2.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2740 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001929	1 retrocopy	retro_cjac_615,
Callithrix jacchus	ENSCJAG00000009064	1 retrocopy	retro_cjac_2740 ,
Mus musculus	ENSMUSG00000032418	1 retrocopy	retro_mmus_1021,