RetrogeneDB ID: retro_cjac_1135

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38423086..38424155(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000006505
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CYP3A21
• Ensembl ID: ENSCJAG00000035708
• Aliases: CYP3A4, CYP3A21, CYPIIIA21
• Description: Cytochrome P450 3A21 [Source:UniProtKB/Swiss-Prot;Acc:O18993]

Sequence

>retro_cjac_1135
GTCCCTATCTTTGCCCAGTATGGAGAGGTGTTGGTGAAAAACCTGAGGCGGGAAGCAGAGAAAGGCAAGGAATCAACATG
AAAGACATCTTTGGGGCCTACAGCATGGATGTGATCACTGACACGTCATTTGGAGTGAACAACAACTCTCTCAACAATCC
ACAAGACCCCTTTGTGGAAAGCACCAAGAAGCTTTTAAGATTTGATGTTTCAGATCCATTCTTTCTCTCAATAACAATCT
TTCCATTCCTTACCCCAATTCTTGAAGCATTAAATATTTCTGTGTTTCCAAGAGATTCTACAAGTTTTTTAAGAAAATCT
ATAAAAAGGATAAAAGAAAGTCGTCTCAAAGATACACATAAGCACCGAGTGGATTTCCTTCAGCTGATGATTGACTCCCA
GAATTCGAAAGAAACTGAGTCCCACAAAGCTCTGTCTGATCTGGAGCTCATGGCCCAATCAATTATCTTCATTTTTACTG
GCTATGAAACCACCAGCAGTAGTCTTTTCTTCGTTATGTATGAACTGGCCACTCACCCTGATGTCCAGCAGAAACCGCAG
GAGGAAATTGATGCAGTTTTACCCAACAAGGCACCAGCCACCTATGATACTGTGCTACAGATGGAGTATCTTGACATGGT
GGTGAATGAAACACTCAGATTATTCCCACTTGCTATGAGACTTGAGAGGATCTGCAAAAAAGATGTTGAAATCAATGGGA
TGTTGATTCCCAAAGGGGTAGTGGTGATGAATCCAAGCTATGCTCTTCACTATGACCCAAAGTACTGGACAGAGACTGAG
AAGTTCCTCCCTGAAAGGTTCAGTAAGAATAACAAGGACAACACAGATAGCACATATACACATCCTTTAGAACTGGACCC
AGAAACTGCATTGGCATGAGGTTTGCTCTCATGAACATGGTACTTGCTCTAATCAGAGTCCTTCAGAACTTGTCCTTCAA
ACCTTGTAAAGAAATACAGATCCCCCTGAAATTATGCTTAGGAGGACTTCTTCAAACAGAAAAACCTATTGTTCTAAAGG
TTGAGTCAAGGGATGGGACTGTAAGTGGA

Alignment

ORF - retro_cjac_1135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.81 %
• Parental protein coverage: 70.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VPIIAQYGEVLVRNLRREAEKGKP-INMKDIFGAYSMDVITGTSFGVNIDSLNNPQDPFVESTKKLLRFD
          VPI.AQYGEVLV.NLRREAEKGK..INMKDIFGAYSMDVIT.TSFGVN..SLNNPQDPFVESTKKLLRFD
Retrocopy VPIFAQYGEVLVKNLRREAEKGKE<INMKDIFGAYSMDVITDTSFGVNNNSLNNPQDPFVESTKKLLRFD

Parental  FLDPFFLSITIFPFLTPILEALNISMFPRDSTSFLRKSIKRIKESRLKDTHKHRVDFLQLMIDSQNSKET
          ..DPFFLSITIFPFLTPILEALNIS.FPRDSTSFLRKSIKRIKESRLKDTHKHRVDFLQLMIDSQNSKET
Retrocopy VSDPFFLSITIFPFLTPILEALNISVFPRDSTSFLRKSIKRIKESRLKDTHKHRVDFLQLMIDSQNSKET

Parental  ESDKALSDLELVAQSIIFIFAGYETTSSTLSFIMYELATHPDVQQKLQEEIDAVLPNKAPATYDTVLQME
          ES.KALSDLEL.AQSIIFIF.GYETTSS.L.F.MYELATHPDVQQK.QEEIDAVLPNKAPATYDTVLQME
Retrocopy ESHKALSDLELMAQSIIFIFTGYETTSSSLFFVMYELATHPDVQQKPQEEIDAVLPNKAPATYDTVLQME

Parental  YLDMVVNETLRLFPLAMRLERVCKKDVEINGVFIPKGVVVMIPSYALHYDPKYWTEPEKFLPERFSKNNK
          YLDMVVNETLRLFPLAMRLER.CKKDVEING..IPKGVVVM.PSYALHYDPKYWTE.EKFLPERFSKNNK
Retrocopy YLDMVVNETLRLFPLAMRLERICKKDVEINGMLIPKGVVVMNPSYALHYDPKYWTETEKFLPERFSKNNK

Parental  DNIDP-YIYTPFGTGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLRLGGLLQTEKPIVLKV
          DN.D...IYT.F.TGPRNCIGMRFALMNM.LALIRVLQN.SFKPCKE.QIPLKL.LGGLLQTEKPIVLKV
Retrocopy DNTDS<HIYTSFRTGPRNCIGMRFALMNMVLALIRVLQNLSFKPCKEIQIPLKLCLGGLLQTEKPIVLKV

Parental  EPRDGTVSG
          E.RDGTVSG
Retrocopy ESRDGTVSG

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	11.45 RPM
SRP051959_heart	0.00 RPM	6.12 RPM
SRP051959_kidney	0.07 RPM	7.12 RPM
SRP051959_liver	0.65 RPM	738.28 RPM
SRP051959_lung	0.02 RPM	9.27 RPM
SRP051959_lymph_node	0.00 RPM	17.08 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.12 RPM
SRP051959_spleen	0.04 RPM	8.38 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1135 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1135 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	ENSCJAG00000035708	1 retrocopy	retro_cjac_1135 ,
Procavia capensis	ENSPCAG00000001718	1 retrocopy	retro_pcap_234,
Ictidomys tridecemlineatus	ENSSTOG00000028864	1 retrocopy	retro_itri_1559,