RetrogeneDB ID: retro_cjac_1086

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38465068..38466144(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PADI6
• Ensembl ID: ENSCJAG00000007733
• Aliases: None
• Description: None

Sequence

>retro_cjac_1086
TCGAAGAAGGCGAGAGTCTACTGGCCCCGAAAAGACAACTCCAGTACCTTTGAGTTGGTGCTAGGGCCCAGCCAGCATGC
CTATACCTTGGCTCTCCTCGGGGACCACTTGAAAGAGACCTTCTACCTTGAAGCTATGGAGTTTCCATCTGCTGAATTCT
CAGGCCTGATCACCTACTCTGTATCCCTGGTGGAGGAGTCTCAAGACCCGTTAATTCCAGAGACTCCGCTGTACAAAGAC
ACTGTGGTGTTTCGGGTGGCTCCCTGCATCTTCATTCCCTGCACCCAGGTGCCTCTGGAGGTTTATCTGTGCAGGGAGCT
GCAGCTGCAGGGTTTTGTGGACACAGTGATGGAGCTGAGTAAGAAGAGCAACAGCCAGGTGGCCTCTGTCTACGAGGACC
CCAGCCGCCTGGGCAGGTGGCTCCAGGATGAGATGGCCTTCTGCTACACCCAGGCGCCCCACAAGACCACATCCTTGATC
CTCGACACGCCTCGAGCCCCCAATCTTGATGAGTTCCCCATGAAATACTCACTGAGCCCCGGTATTGGCTACATGATCCA
CGACACTGAAGACCATAAAGTGGCCAGCATGGATTCCATCGGGAACGTGATGGTGTCCCCACCTGTCAAGGTCCAAGGGA
AAGAATACCCCCTGGGCAGAGTCCTCATTGGCAGCAGCTTTTACCCCAGCATGGAGGGCCGGGCCATGAGTAAGACCCTC
CGAGACTTCCTCTATGCCCAGCAGGTCCAAGCACTGGTGGACTCTACTCAGATTGGCTGATGACCGGCCACGTGGATGAG
TTCATGTGTTTCATACCCACAGATGAGAAGAGTGAGGGCAAAAAGGGCTTCCAGCTGCTCCTGGCCAGCCCCGGCACCTG
CTACAAACTCTTCTAAGAGAAACAGAAGGAAGGCTATGGTGATGCTTTTCTGTTTGATGGAGTTAGAGCAGATCAGCTCC
TGTCTAACAGAACGGAAGCCAAAACAATTGACCAGCTTCTGGCTGATGAAAGCCTGAGGAAGCAGAATGAATACGTGGAG
AAGTGCACTCACCTGAACCATGACATCCTGAAGACA

Alignment

ORF - retro_cjac_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.68 %
• Parental protein coverage: 51.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKKARVYWPRKDNSSTFELVLGPSQYAYTLALLGDHLKETFYLEAMEFPSAEFSGLITYSVSLVEESQDP
          SKKARVYWPRKDNSSTFELVLGPSQ.AYTLALLGDHLKETFYLEAMEFPSAEFSGLITYSVSLVEESQDP
Retrocopy SKKARVYWPRKDNSSTFELVLGPSQHAYTLALLGDHLKETFYLEAMEFPSAEFSGLITYSVSLVEESQDP

Parental  LIPETPLYKDTVVFRVAPCIFIPCTQVPLEVYLCRELQLQGFVDTVMELSKKSNSQVASVYEDPSRLGRW
          LIPETPLYKDTVVFRVAPCIFIPCTQVPLEVYLCRELQLQGFVDTVMELSKKSNSQVASVYEDPSRLGRW
Retrocopy LIPETPLYKDTVVFRVAPCIFIPCTQVPLEVYLCRELQLQGFVDTVMELSKKSNSQVASVYEDPSRLGRW

Parental  LQDEMAFCYTQAPHKTTSLILDTPRAPNLDEFPMKYSLSPGIGYMIHDTEDHKVASMDSIGNVMVSPPVK
          LQDEMAFCYTQAPHKTTSLILDTPRAPNLDEFPMKYSLSPGIGYMIHDTEDHKVASMDSIGNVMVSPPVK
Retrocopy LQDEMAFCYTQAPHKTTSLILDTPRAPNLDEFPMKYSLSPGIGYMIHDTEDHKVASMDSIGNVMVSPPVK

Parental  VQGKEYPLGRVLIGSSFYPSMEGRAMSKTLRDFLYAQQVQAPVE-LYSDWLMTGHVDEFMCFIPTDDKSE
          VQGKEYPLGRVLIGSSFYPSMEGRAMSKTLRDFLYAQQVQA.V..LYSDWLMTGHVDEFMCFIPTD.KSE
Retrocopy VQGKEYPLGRVLIGSSFYPSMEGRAMSKTLRDFLYAQQVQALVD<LYSDWLMTGHVDEFMCFIPTDEKSE

Parental  GKKGFQLLLASPGACYKLFQEKRKEGYGDAFLFDGVRADQLLSNSKREAKTIDQLLADESLRKQNEYVEK
          GKKGFQLLLASPG.CYKLF.EK.KEGYGDAFLFDGVRADQLLSN...EAKTIDQLLADESLRKQNEYVEK
Retrocopy GKKGFQLLLASPGTCYKLF*EKQKEGYGDAFLFDGVRADQLLSN-RTEAKTIDQLLADESLRKQNEYVEK

Parental  CIHLNHDILKT
          C.HLNHDILKT
Retrocopy CTHLNHDILKT

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	0.04 RPM
SRP051959_heart	0.00 RPM	0.04 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.04 RPM
SRP051959_lung	0.00 RPM	0.15 RPM
SRP051959_lymph_node	0.02 RPM	0.62 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.00 RPM	0.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1086 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1086 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1086 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007733	2 retrocopies	retro_cjac_1086 , retro_cjac_1210,
Sus scrofa	ENSSSCG00000003484	1 retrocopy	retro_sscr_1118,