RetrogeneDB ID: retro_cjac_4215

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:109557405..109558441(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033188
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PA2G4
• Ensembl ID: ENSCJAG00000011811
• Aliases: None
• Description: None

Sequence

>retro_cjac_4215
TTGCTGAGCCTGTGTGAGAAAGGTGATGCCATGATTATGGAAGAAACAGGGAAAATCTTCAAGAAAGAAAAGGAAATGAA
GAAAGGTATTGCTTTTCCCACCAGCATTTCGGTAAATAATTGTGTACGTCACTTCTCCCCTTTGAAGAGCGACCAGGATT
ATATTCTCAAGGAAGGTGACTTGGTAAAAATTGACCTTGGGGTCCATGTGGATGGCTTCATCGCTAATGTAGCTCATACT
TTTGTGGTTGATATAGCTCAGGTGACCCAAGTAACCGGGAGGAAAGCAGATGTTATTAAGGCAACTCACCTTTGTGCCGA
AGCTGCCCTACAGTTGGTCAAACCTGGAAACCAGAATACACAAGTGACAGAAGCCTGGAACAAAGTTGCCCACTCATTTA
ACTGCACGCCAGTAGAAGGTATGCTGTCACACCAGTTGAAGCAGCATGTCATTGATGGAGAAAAAACCATTATCCAGAAT
CCCACAGACCAGCAGAAGAAGGACCATGAAAAGTTGAATTTGAGGTACATGAAGTATATGCTGTGGATGTTCTCGTCAGC
TCAGGAGAGGGCAAGGCCAAGGATGCAGGACAGAGAACCACTATTTATAAACGAGACCCCTCTAAACAGTATGGACTGAA
AATAAAAACTTCATGTGCCTTCTTCAGTGAGGTGGAAAGGCGTTTTGATGCCATGCCATTTACTTTAAGAGCATTTGAAG
ATGAGAAGAAGGCTCGGATGGGTGTGGTAGAGTGCATCAAACATGAACTGCTGCAACCATTTAATATTCTCTATGAGAAG
GAGGGTGAATTTGTTGCCCAGTTTAAATTTACAGTTCTGCTCATGTCCAACGGCCCCATGCGGATAACCAGTGGTCCCTT
TGAGCCTGACATGGAGGTCCAGGATGCAGAGCTAAAGGCCCACCTCCAGAGTTCTGCAAGTCAAAAAACCCAGAAAAAGA
AAAAAAAAAGAAGGCCTCGAAGACTGCAGAGAATGCCACCAGTGAGGAAACATTAGAAGAAAATGAAGCTGGGGAC

Alignment

ORF - retro_cjac_4215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.92 %
• Parental protein coverage: 88.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLSLCEKGDAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHV
          .LSLCEKGDAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCV.HFSPLKSDQDYILKEGDLVKIDLGVHV
Retrocopy LLSLCEKGDAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCVRHFSPLKSDQDYILKEGDLVKIDLGVHV

Parental  DGFIANVAHTFVVDVAQGTQVTGRKADVIKAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCTPIEG
          DGFIANVAHTFVVD.AQ.TQVTGRKADVIKA.HLCAEAAL.LVKPGNQNTQVTEAWNKVAHSFNCTP.EG
Retrocopy DGFIANVAHTFVVDIAQVTQVTGRKADVIKATHLCAEAALQLVKPGNQNTQVTEAWNKVAHSFNCTPVEG

Parental  MLSHQLKQHVIDGEKTIIQNPTDQQKKDHE-KAEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSK
          MLSHQLKQHVIDGEKTIIQNPTDQQKKDHE.K.EFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSK
Retrocopy MLSHQLKQHVIDGEKTIIQNPTDQQKKDHE<KVEFEVHEVYAVDVLVSSGEGKAKDAGQRTTIYKRDPSK

Parental  QYGLKMKTSRAFFSEVERRFDAMPFTLRAFEDEKKARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTV
          QYGLK.KTS.AFFSEVERRFDAMPFTLRAFEDEKKARMGVVEC.KHELLQPFN.LYEKEGEFVAQFKFTV
Retrocopy QYGLKIKTSCAFFSEVERRFDAMPFTLRAFEDEKKARMGVVECIKHELLQPFNILYEKEGEFVAQFKFTV

Parental  LLMPNGPMRITSGPFEPDLYKSEMEVQDAELKALLQSSASRKTQKK-KKKKASKTAENATSGETLEVNEA
          LLM.NGPMRITSGPFEPD......E...A.L.....S.......KK.KKKKASKTAENATS.ETLE.NEA
Retrocopy LLMSNGPMRITSGPFEPDMEVQDAELK-AHLQS---SASQKTQKKK<KKKKASKTAENATSEETLEENEA

Parental  GD
          GD
Retrocopy GD

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	0.07 RPM	22.96 RPM
SRP051959_heart	0.04 RPM	19.68 RPM
SRP051959_kidney	0.07 RPM	21.39 RPM
SRP051959_liver	0.04 RPM	19.82 RPM
SRP051959_lung	0.05 RPM	23.21 RPM
SRP051959_lymph_node	0.02 RPM	23.97 RPM
SRP051959_skeletal_muscle	0.02 RPM	32.32 RPM
SRP051959_spleen	0.02 RPM	20.88 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4215 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4215 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4215 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Callithrix jacchus	ENSCJAG00000011811	2 retrocopies	retro_cjac_4214, retro_cjac_4215 ,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Pan troglodytes	ENSPTRG00000005076	6 retrocopies	retro_ptro_1289, retro_ptro_1389, retro_ptro_1940, retro_ptro_2471, retro_ptro_2846, retro_ptro_3263,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,