RetrogeneDB ID: retro_cjac_4163

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:49915101..49917201(-)
• Located in intron of: ENSCJAG00000000368

Retrocopy information

• Ensembl ID: ENSCJAG00000037743
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008172
• Aliases: None
• Description: None

Sequence

>retro_cjac_4163
GCTGAGAAGAAAGCCAAGGTCATTGCAGTAATGAATGCTGTGGAAGCAAACCAGGGTTCCTGGGAGTCTCAGAAGGTGGA
GGAGGCCAGCCCTCCTGCTGTGCAGCAGCCCACTGACCCTGCATCCCCCACTGTGGCCACCATGCCAGAGCCCGTGGGGG
CCGATGCTGGGGACAAGAATGCTACCAAAGCAGGCGATGATAAGCTGGAGTAGGAGGACGGCCGGGGCTTTGGCATTGGG
GAGCTGGTGTGGGGGAAACTGCAGGGCTTCTCGTGGTGGCCAGGCCACATTGTGTCTTGGTGGATGACAGGCCGGAGCCG
AGCAGCTGAAGGCACCCGCTGGGTCATGTGGTTCGGAGATGGCTAGTTCTCAGTGGTGTGTGTTGAGAAGCTGATGCCGC
TGAGCTCGTTTTGCAGTGCGTTCCACCAGGCCATGTAACACGAGCAGCCCATGTACCGCAAAGCCATCTATGAGGTCCTG
CTGGTGGCCAGCAGCCGTGCGGGGAAGCTGTTCCCAGTGTGCCACGACAGTGACGAGAGTGACACTGCCAAGGCCGTGGA
CGTGCAGAACAAGCAGATGATTGAATGGGCCCTGGGGGTCTTCCAGCCCTCTGGTCCCAAGGGCCTGGAGCCACCAGAAG
GGGAAAAGAATTCCTACAAAGAAGTGTACACGGACATGTGGGTGGAACCTGAGGCAGCTGCCTAGGCACCACCTCCACCA
GCCAAAAAGCCCTGGAAGAGCACAACGGAGAAGCCCAAGGTCAAGGAGATCATCGATGATGAGTGCACAAGAGAGCGGCT
GATGTACGAGGTGCGGCAGAAGTGCCAGAACATGGAGGACATCTGCATCTCCTGTGGGAGCTTCAACGTCACCCTGGAAC
ACCCCCTCTTCATTGGAGGAATGTGCCAAAACTGCAAGAACTGCTTTCTGGAGTGTGCATACCAGTACGATGACGACGGC
TATCAGTCCTACTGCACCATCTGCTGCGGGGGCCGAGAAGTGCTTATGAGCGGGAACAACAACTGCTGCAGGTGCTTTTG
TGTGGAATGTGTGGACCTCTTGGTGGGGCCGGGGGCTGCCCAGGCAGCCATTAAGGAAGACCCCGGGAACTGCTACATGT
GTGGGCACAAGGGCACCTACGGGCTGCTGCGGCGGCAAGACGACTGGCCCTCCTGGCTCCAGATGTTCTTCGCTAATAAC
CACGACCAGGAATTTGACCCTCTAAAGGTTTACCCACCTGTCCCAGCTGAGAAGAGGAAGCCCATTCGGGTGCTGTCTCT
CTTTGACAGAATTGCTACAGGGCTCCTGGTGCTGAAGGACTTGGGCATTCAGGTGGACCGCTACATTGCCTCGGAGGTGT
GTGAGGGCTCCATCACGGTGGGCATGGTGCCGCACCAGGGGAAGATCATGTACGTTGGGGACGTCCGCAGCGTCACACAG
AAGCATATCCAGGAGTGGGGCCCATTTGATCTTGTAATTGGGGGCAGTCCCTGCAATGACCTCTCCATTGTCAACCCTGC
TCGCAAGGGCCTCTGCGAGGGCACTGGCGGGCTCTTCTTTGAGTTCTACCGCCTCCTGCATGATGCGCGGCCCAAGGAGG
GAGATGACCGCCCCTTCTTCTGGCTCTTTGAGAATGTGGTGGCCATGGGCGTTGGTGACAAGAGGGACATCTCGCGATTT
CTCGAGTCCAACCCTGTGATGATTGATGCCAAAGAAGTGTCAGCTGCACACAGGGCCCGCTACTTCTGGGGTAACCTTCC
CGGTATGAACAGGCCATTGGCATCCACTGTGAATGGTAAGCTGGAGCTGCAGGAGTGTCTGGAGCATGGAAGGATAGCCA
AGTTCAGCAAAGTGAGGACCATTACTACAAGGTCAAACTCCATAAAGCAAGGCGTAGACCAGCATTTCCCCATCTTCATG
AATGAGAAAGAGGACATCCTATGGCGCACTGAAATGGAAAGGGTATTTGGTTTCCCTGTCCACTATGCCGACGTCTCCAA
CATGAGCCGCTTGGCGAGGCAGAGACTGCTGGGACGGTCGTGGAGCGTGCCAGTCATCCGCCACCTCTTCGCTCCGCCGA
AGGAGTATTTTGCGTGTGTG

Alignment

ORF - retro_cjac_4163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.71 %
• Parental protein coverage: 96.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEKKAKVIAVMNAVEENQGSGESQKVEEASPPAVQQPTDPASPTVATTPEPVGADAGDKNATKAGDDEPE
          AEKKAKVIAVMNAVE.NQGS.ESQKVEEASPPAVQQPTDPASPTVAT.PEPVGADAGDKNATKAGDD..E
Retrocopy AEKKAKVIAVMNAVEANQGSWESQKVEEASPPAVQQPTDPASPTVATMPEPVGADAGDKNATKAGDDKLE

Parental  YEDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRAAEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSA
          .EDGRGFGIGELVWGKL.GFSWWPG.IVSWWMTGRSRAAEGTRWVMWFGDG.FSVVCVEKLMPLSSFCSA
Retrocopy *EDGRGFGIGELVWGKLQGFSWWPGHIVSWWMTGRSRAAEGTRWVMWFGDG*FSVVCVEKLMPLSSFCSA

Parental  FHQATYNKQPMYRKAIYEVLQVASSRAGKLFPVCHDSDESDTAKAVEVQNKQMIEWALGGFQPSGPKGLE
          FHQA....QPMYRKAIYEVL.VASSRAGKLFPVCHDSDESDTAKAV.VQNKQMIEWALG.FQPSGPKGLE
Retrocopy FHQAM*HEQPMYRKAIYEVLLVASSRAGKLFPVCHDSDESDTAKAVDVQNKQMIEWALGVFQPSGPKGLE

Parental  PPEEEKNPYKEVYTDMWVEPEAAAYAPPPPAKKPRKSTTEKPKVKEIIDER-TRERLVYEVRQKCRNIED
          PPE.EKN.YKEVYTDMWVEPEAAA.APPPPAKKP.KSTTEKPKVKEIID...TRERL.YEVRQKC.N.ED
Retrocopy PPEGEKNSYKEVYTDMWVEPEAAA*APPPPAKKPWKSTTEKPKVKEIIDDECTRERLMYEVRQKCQNMED

Parental  ICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVEC
          ICISCGS.NVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLM.GNNNCCRCFCVEC
Retrocopy ICISCGSFNVTLEHPLFIGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMSGNNNCCRCFCVEC

Parental  VDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRRDDWPSRLQMFFANNHDQEFDPPKVYPPVPAEKRK
          VDLLVGPGAAQAAIKEDP.NCYMCGHKGTYGLLRR.DDWPS.LQMFFANNHDQEFDP.KVYPPVPAEKRK
Retrocopy VDLLVGPGAAQAAIKEDPGNCYMCGHKGTYGLLRRQDDWPSWLQMFFANNHDQEFDPLKVYPPVPAEKRK

Parental  PIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVTQKHIQEWGPFD
          PIRVLSLFD.IATGLLVLKDLGIQVDRYIASEVCE.SITVGMV.HQGKIMYVGDVRSVTQKHIQEWGPFD
Retrocopy PIRVLSLFDRIATGLLVLKDLGIQVDRYIASEVCEGSITVGMVPHQGKIMYVGDVRSVTQKHIQEWGPFD

Parental  LVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVSDKRDISRF
          LVIGGSPCNDLSIVNPARKGL.EGTG.LFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGV.DKRDISRF
Retrocopy LVIGGSPCNDLSIVNPARKGLCEGTGGLFFEFYRLLHDARPKEGDDRPFFWLFENVVAMGVGDKRDISRF

Parental  LESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNDKLELQECLEHGRIAKFSKVRTITTRSNSIKQ
          LESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVN.KLELQECLEHGRIAKFSKVRTITTRSNSIKQ
Retrocopy LESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTVNGKLELQECLEHGRIAKFSKVRTITTRSNSIKQ

Parental  GKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSNMSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV
          G.DQHFP.FMNEKEDILW.TEMERVFGFPVHY.DVSNMSRLARQRLLGRSWSVPVIRHLFAP.KEYFACV
Retrocopy GVDQHFPIFMNEKEDILWRTEMERVFGFPVHYADVSNMSRLARQRLLGRSWSVPVIRHLFAPPKEYFACV

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	0.00 RPM	10.61 RPM
SRP051959_heart	0.00 RPM	17.58 RPM
SRP051959_kidney	0.04 RPM	21.88 RPM
SRP051959_liver	0.00 RPM	10.87 RPM
SRP051959_lung	0.02 RPM	16.79 RPM
SRP051959_lymph_node	0.00 RPM	21.51 RPM
SRP051959_skeletal_muscle	0.02 RPM	20.03 RPM
SRP051959_spleen	0.04 RPM	24.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4163 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4163 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4163 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008172	2 retrocopies	retro_cjac_4163 , retro_cjac_899,
Microcebus murinus	ENSMICG00000004108	2 retrocopies	retro_mmur_1086, retro_mmur_797,
Monodelphis domestica	ENSMODG00000015850	1 retrocopy	retro_mdom_859,
Oryctolagus cuniculus	ENSOCUG00000024688	1 retrocopy	retro_ocun_564,