RetrogeneDB ID: retro_cjac_1138

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38796563..38797925(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031692
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AKT2
• Ensembl ID: ENSCJAG00000014574
• Aliases: None
• Description: None

Sequence

>retro_cjac_1138
ATGAACAAGGTGTCTGTCATCAAAGAAGGCTAGCTCCACAAGCGCGGTGAATACATCAAGACCTGGAGGCCACGGTACTT
CCTGCTAAAGAGTGACAGCTCCTTCATTGGGTACAAGGAGAGGTCCGAGGCCCCTGATCAGACCCTGCCCCCTTAAACAA
CTTCTCTGTAGCAGAATGCCAGCTGATAAAGACTGAGAGGCCGAGGCCCAACACCTTTGTCATACACTGCCTGCAGTGGA
CCACAGTCATTGAGAGGACCTTCCATGTGGATTCTCCAGATGAGAGGGAGGAGTGGATGCGAGCCATCCAGATGGTCGCC
AACAGCCTCAAGCAGCGGGCCCTGGGCGAGGACCCCATGGACTACAAGTGTGGCTCCCCCAGTGACTCCTCTGTGGCTGA
GGAGTTGGAAGTGGCAGTCAGCAAGGCACGGGCCAAAGTGACCATGAATGACTTCGACTATCTCAAACTCCTTGCCAAGG
GAACCTTTGGCAAAGTCATCCTGGTGCGGGGGAAGGCCACCGGCAGCTACTACACCATGAAGATCCTGCGGAAGGAAGTC
ATCATTGCCAAGGATGAAGTCGTTCACACAATCAGCGAGAGCCGGGTCCTCCAGAACACCAGGCACCCATTCCTCACTGC
ACTGAAGTATGCCTTCCAGACCCACCACTGTCTGTGCTTCGTGATGGAGTACGCCAACGATGGCGAGCTGTTCTTCCACC
TGTCCCGGGAGTGTGTCTTCACAGAGGAGCGGGCACGGTTTTATGGTGCAGAGATCGTCTCAGCTCTTGAGTACTTGCAC
TCTTGGGACATGGTGTACCGCGACATCAAGCTGGAAAACCTCATGCTGGACAAAGATGGCCACATCAAGATCACTGACTT
TGGCTCTGCAAAGAAGGCATCGGTGATTGGGCCACCATGAAAACCTTCTGTGGGACTCTGGAGTATCTGGCGCCTGAGGT
GCTGGAGGAAAACTATTGCCGGGCAGTGGACTGGTGGGGGCTGGGTGTGGTCATGTACGAGATGATGTGTGGCCGCCTAT
CCTTCTACAACCAGAACCACAAGCGCCTCTTCAAGCTCATCCTCGTGGAGGAGATCCGTTTCCTGTGCACGCTTAGCCCC
GAGGCCAAGTCGGGCTGCTTAAGAAGGACCCCAAGCAGAGGCTTGGGGGGCCCAGCGATGCCCAGGAGGTCATGGAGCAC
GGGTTGTTCCTCAGCATCAACTGGCAGGATGTGGTCCAGAAGAAGCTCCTGCCACCCTTCAAACCTCAGGTCACGACTGA
GGTCGACACATGGTACTTGAATGATGAATTCACCGCCCAGTCCATCACAATCACACCCCCTGACTGCTATGACAGCCTGG
GC

Alignment

ORF - retro_cjac_1138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNEVSVIKEGWLHKRGEYIKTWRPRYFLLKSDGSFIGYKERPEAPDQTLPP-LNNFSVAECQLMKTERPR
          MN.VSVIKEG.LHKRGEYIKTWRPRYFLLKSD.SFIGYKER.EAPDQTLPP.LNNFSVAECQL.KTERPR
Retrocopy MNKVSVIKEG*LHKRGEYIKTWRPRYFLLKSDSSFIGYKERSEAPDQTLPP<LNNFSVAECQLIKTERPR

Parental  PNTFVIRCLQWTTVIERTFHVDSPDEREEWMRAIQMVANSLKQRALGEDPMDYKCGSPSDSSVAEEMEVA
          PNTFVI.CLQWTTVIERTFHVDSPDEREEWMRAIQMVANSLKQRALGEDPMDYKCGSPSDSSVAEE.EVA
Retrocopy PNTFVIHCLQWTTVIERTFHVDSPDEREEWMRAIQMVANSLKQRALGEDPMDYKCGSPSDSSVAEELEVA

Parental  VSKARAKVTMNDFDYLKLLGKGTFGKVILVREKATGRYYAMKILRKEVIIAKDEVAHTVTESRVLQNTRH
          VSKARAKVTMNDFDYLKLL.KGTFGKVILVR.KATG.YY.MKILRKEVIIAKDEV.HT..ESRVLQNTRH
Retrocopy VSKARAKVTMNDFDYLKLLAKGTFGKVILVRGKATGSYYTMKILRKEVIIAKDEVVHTISESRVLQNTRH

Parental  PFLTALKYAFQTHDRLCFVMEYANGGELFFHLSRERVFTEERARFYGAEIVSALEYLHSRDVVYRDIKLE
          PFLTALKYAFQTH..LCFVMEYAN.GELFFHLSRE.VFTEERARFYGAEIVSALEYLHS.D.VYRDIKLE
Retrocopy PFLTALKYAFQTHHCLCFVMEYANDGELFFHLSRECVFTEERARFYGAEIVSALEYLHSWDMVYRDIKLE

Parental  NLMLDKDGHIKITDFG-LCKEGISDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRL
          NLMLDKDGHIKITDFG.LCKEGI.D.ATMKTFCGT.EYLAPEVLE.N.Y.RAVDWWGLGVVMYEMMCGRL
Retrocopy NLMLDKDGHIKITDFG<LCKEGIGDWATMKTFCGTLEYLAPEVLEEN-YCRAVDWWGLGVVMYEMMCGRL

Parental  PFYNQDHERLFELILMEEIRFPRTLSPEAKSLLAGLLKK-DPKQRLGGGPSDAQEVMEHRFFLSINWQDV
          .FYNQ.H.RLF.LIL.EEIRF..TLSPEAKS...G.L...DPKQRL.GGPSDAQEVMEH..FLSINWQDV
Retrocopy SFYNQNHKRLFKLILVEEIRFLCTLSPEAKS---GCLRR<DPKQRL-GGPSDAQEVMEHGLFLSINWQDV

Parental  VQKKLLPPFKPQVTSEVDTRYFDDEFTAQSITITPPDRCECLG
          VQKKLLPPFKPQVT.EVDT.Y..DEFTAQSITITPPD....LG
Retrocopy VQKKLLPPFKPQVTTEVDTWYLNDEFTAQSITITPPDCYDSLG

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	3.82 RPM	9.23 RPM
SRP051959_heart	4.81 RPM	15.42 RPM
SRP051959_kidney	2.97 RPM	13.07 RPM
SRP051959_liver	2.64 RPM	23.42 RPM
SRP051959_lung	5.08 RPM	13.62 RPM
SRP051959_lymph_node	5.09 RPM	12.88 RPM
SRP051959_skeletal_muscle	4.43 RPM	31.29 RPM
SRP051959_spleen	5.00 RPM	12.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1138 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1138 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1138 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014574	1 retrocopy	retro_cjac_1138 ,
Mus musculus	ENSMUSG00000004056	1 retrocopy	retro_mmus_694,
Sus scrofa	ENSSSCG00000002989	2 retrocopies	retro_sscr_1164, retro_sscr_1200,