RetrogeneDB ID: retro_cjac_3972

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286459.1:140457..141485(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCAMP3
• Ensembl ID: ENSCJAG00000008486
• Aliases: None
• Description: None

Sequence

>retro_cjac_3972
GTGGCTCAGAGCAGAGACCGCAGAAACCCATCTGCCGGGTCCAGCGAGCTTGACAACTCCTTTCAGGACCCAGCTGTGAT
CCAGCACCGACCCAGCTGGCAGCATGCCATGCTTGACATCTACAACCCTTTTGAGACCCGGGAGCCACTGCCAGCCTATG
GGCTTCCAGCCCCTGCTTTATTGCCTCCACCCTCAGCTCCCTCCTTGAAATCCTCGAGAAAGCTCAGCCCCACAGAATCT
AAGAACTATGGCTCCTACAGCACTCAGGCCTCAGCTGCAGCAGCCACAGCTGAGCTGCTAAAGAAACAGGAGGAGCTCAA
CTGGAAGGCAGAGGAGGTGGACCGAAAGGAGTGAGAGCTGCAGCATGCTATCTGGGGGGCCCTGCTACTCGACAGAACAA
TTGGCCCCCTCTACCTTCTTTTCATCCAGTTCTGCCCTGCTTTTTCCAGGACATCTCCATGGAGATCCTCCAAGAATTTC
CAGAAGACTGTACCCACCATGTACTACCTCTGGATGTGCAGCTCTCTGGCTCTTCTCCTGAACTTTCTTGCCTGCCTGGC
CAAGTTCTGTGTGGAAACCAGAAGTGGCTCAGGCTTTGGGCTTTCCATTCTCTGGATCCTCCTTTTCACACCCTGCTCCC
TTGTCTACTGGTACTGCCCCATGTATAAGCCTTTCCAGAGTGACAGTTCATTCAGTTTCTTCATTTTCTTTGCCCAGGAT
GTGCTGTTTGTCCTCCAGGCCATTGGTATCCCAGGTTGGGGATTCAGTGGCTGGATCTCTGCTCTGGAGGTGCTGATATC
AGTCCAGCAGTAGCTGTGCTCATGTTGCTGGTCGCCCTTCTCTTCACTGGCATTGCTGTGCTAGGAATTGTCATGCTAAA
ACGGATCCACTCCTTGTACCACTGCACAGGTGCCAGCTTTCAGACGGCCCAGCAAGAATTTGCTGCTGGTGTGTTCTCCA
ATACTGCGGTGTGAACCGCAGCTGCCAATGCAGCTGCTGGGGCTGCTGAAAATGCCTTCCGGGGCCCA

Alignment

ORF - retro_cjac_3972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAQSRDGGNPFAEPSELDNPFQDPAVIQHRPSRQYATLDVYNPFETQEPLPAYEPPAPAPLPPPSAPSLQ
          .AQSRD..NP.A..SELDN.FQDPAVIQHRPS.Q.A.LD.YNPFET.EPLPAY..PAPA.LPPPSAPSL.
Retrocopy VAQSRDRRNPSAGSSELDNSFQDPAVIQHRPSWQHAMLDIYNPFETREPLPAYGLPAPALLPPPSAPSLK

Parental  SSRKLSPTEPKNYGSYSTQASAAAATAELLKKQEELNRKAEELDRRERELQHAA-LGGTATRQNNWPPLP
          SSRKLSPTE.KNYGSYSTQASAAAATAELLKKQEELN.KAEE.DR.E.ELQHA..LGG.ATRQNNWPPLP
Retrocopy SSRKLSPTESKNYGSYSTQASAAAATAELLKKQEELNWKAEEVDRKE*ELQHAI<LGGPATRQNNWPPLP

Parental  SFCPVQPCFFQDISMEIPQE-FQKTVSTMYYLWMCSTLALLLNFLACLAKFCVETSSGSGFGLSILWILL
          SF.PV.PCFFQDISMEI.QE.FQKTV.TMYYLWMCS.LALLLNFLACLAKFCVET.SGSGFGLSILWILL
Retrocopy SFHPVLPCFFQDISMEILQE>FQKTVPTMYYLWMCSSLALLLNFLACLAKFCVETRSGSGFGLSILWILL

Parental  FTPCSLVCWYRPMYKAFRSDSSFNFFVFFFIFFAQDVLFVLQAIGIPGWGFSGWISALEVL-HISPAVAV
          FTPCSLV.WY.PMYK.F.SDSSF.FF.FF....AQDVLFVLQAIGIPGWGFSGWISALEVL..ISPAVAV
Retrocopy FTPCSLVYWYCPMYKPFQSDSSFSFFIFF----AQDVLFVLQAIGIPGWGFSGWISALEVL<DISPAVAV

Parental  LMLLVALLFTGIAVLGIVMLKRIHSLYRRTGASFQKAQQEFAAGVFSNPAVRTAAANAAAGAAENAFRGP
          LMLLVALLFTGIAVLGIVMLKRIHSLY..TGASFQ.AQQEFAAGVFSN.AV.TAAANAAAGAAENAFRGP
Retrocopy LMLLVALLFTGIAVLGIVMLKRIHSLYHCTGASFQTAQQEFAAGVFSNTAV*TAAANAAAGAAENAFRGP

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	8.16 RPM
SRP051959_heart	0.00 RPM	8.72 RPM
SRP051959_kidney	0.02 RPM	11.38 RPM
SRP051959_liver	0.00 RPM	7.02 RPM
SRP051959_lung	0.00 RPM	11.09 RPM
SRP051959_lymph_node	0.00 RPM	11.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	11.18 RPM
SRP051959_spleen	0.00 RPM	9.89 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3972 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3972 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	ENSCJAG00000008486	1 retrocopy	retro_cjac_3972 ,