RetrogeneDB ID: retro_cjac_523

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:45569909..45570875(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALR1
• Ensembl ID: ENSCJAG00000007988
• Aliases: None
• Description: galanin receptor 1 [Source:HGNC Symbol;Acc:4132]

Sequence

>retro_cjac_523
CTGTTCCGCATCGGCGCTGTTCCACTTCGCCACGCTGGTAGTGTTGGCCTGATCTTGGCGCTGGGCGTGCTGGGCAACAG
CCTGGTTATCACCGCTCTGGTGTGCAGCAAGCCGGGCAGGCCGAAAAGCACCACCGACCTGTTCATCCTTAACCCGAGTA
TCGCCGACCTGACCTAACTGCTCTTCTGCATCCCCTTCCAGGGCACCGTGTACGCGCTGCCCACCTGGGGTGCTGGGCGC
CTTCATCTGTTGTTCACCCACTACTTCTTCACTGTGTCCATGCTGATAAGCATCTTTACGCTGACCGCGATGTCCCTGGA
TCGCTACATGGCCATCGTGCACTCGCGGCGCTCCTCCTCGCTCAGAGTGTCCAGCAACTCGCTGCTGGGCGTGGGCTGCA
TCTGGGCGCTGTCCATCGCCATGGCCTCGCCCGTGGCCTACCACCAGGGCCTCTTCCACCCGCGCGCCAGCAACCAGACC
TTCTGCTGGGAGGAGTGGCCCGACCCTCGCCACAAGAAGGCCTACGTGTTGTGCACCTTCGTCTTCGGCTACCTGCTGCC
GCTCCTGCTCATCAGCTTCTGCTATGCCAAAGTCCTTAATCATTTGCATAAAAAGTTGAAGAACAGGTCAAAGAAGTCTC
AAATATCCAAGAAAAAGACTGCACAGACGATTCTTGTGGTGGTGTTTGGAATCTCCTGGCTGCTTCACCACATCATTCAT
CTCTGGGTTGAGTTTGGAGTTTTCCCACTGACACCGGCTTCCTTCTTCTTCAGAATCACTGTCCACTGCCTGGCGTACAG
CAATTCCTCGGTGAATCCTATCATATATGCATTTCTCTCTGAAAATTTCAGGAAGGCTTATAAGCAAGTGTTCAAGTGTC
ACCTTCACAAAGATTCAGATCTGAATGACAATAAAGAAAACAAAAGTCGACTAGACACCCCAACATCAACCAATTGTACC
CATGTG

Alignment

ORF - retro_cjac_523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.11 %
• Parental protein coverage: 92.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LFRIGAE-NFATLVVF-GLIFALGVLGNSLVITVLARSKPGKPRSITNLFILNLSIADLAYLLFCIPFQA
          LFRIGA...FATLVV..GLI.ALGVLGNSLVIT.L..SKPG.P.S.T.LFILN.SIADL..LLFCIPFQ.
Retrocopy LFRIGAV>HFATLVVL<GLILALGVLGNSLVITALVCSKPGRPKSTTDLFILNPSIADLT*LLFCIPFQG

Parental  TVYALPTW-VLGAFIC-KFTHYFFTVSMLVSIFTLAAMSVDRYVAIVHSRRSSSLRVSRNALLGVGCIWA
          TVYALPTW.VLGAFIC..FTHYFFTVSML.SIFTL.AMS.DRY.AIVHSRRSSSLRVS.N.LLGVGCIWA
Retrocopy TVYALPTW>VLGAFIC<LFTHYFFTVSMLISIFTLTAMSLDRYMAIVHSRRSSSLRVSSNSLLGVGCIWA

Parental  LSIAMASPVAYHQGLFHPRASNQTFCWEQWPDPRHKKAYVVCTFVFGYLLPLLLISFCYAKVLNHLHKKL
          LSIAMASPVAYHQGLFHPRASNQTFCWE.WPDPRHKKAYV.CTFVFGYLLPLLLISFCYAKVLNHLHKKL
Retrocopy LSIAMASPVAYHQGLFHPRASNQTFCWEEWPDPRHKKAYVLCTFVFGYLLPLLLISFCYAKVLNHLHKKL

Parental  KSMSKKSETSKKKTAQTILVVVVVFGISWLPHHIIHLWVEFGVFPLTPASFFFRITAHCLAYSNSSVNPI
          K..SKKS..SKKKTAQTIL..VVVFGISWL.HHIIHLWVEFGVFPLTPASFFFRIT.HCLAYSNSSVNPI
Retrocopy KNRSKKSQISKKKTAQTIL--VVVFGISWLLHHIIHLWVEFGVFPLTPASFFFRITVHCLAYSNSSVNPI

Parental  IYAFLSENFRKAYKQVFKCHLRKDSDLNDNKENKSRIDTPPSTNCTHV
          IYAFLSENFRKAYKQVFKCHL.KDSDLNDNKENKSR.DTP.STNCTHV
Retrocopy IYAFLSENFRKAYKQVFKCHLHKDSDLNDNKENKSRLDTPTSTNCTHV

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	0.20 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 RPM	0.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_523 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_523 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_523 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007988	1 retrocopy	retro_cjac_523 ,