RetrogeneDB ID: retro_cjac_1605

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:58694104..58695538(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SWAP70
• Ensembl ID: ENSCJAG00000011252
• Aliases: None
• Description: None

Sequence

>retro_cjac_1605
AAAAAAAACCTCACAAAAGAATCCCCTGCTCATTACAGAAGATGATGCATTTAAAGTATGGGTTATTTTCAACTTTGTAT
CTGAGGCCAAGTATCCATTAATTATTGTGACAGAAGAGATTGAATACCTGCTTAAGAAGCTTACAGAAGCTATGGGAGGA
GGTTGGCAGCAAGAACAATTTGAACATTATAAAGTCAACTTTGATGACAGTAAAGATGGCGTGGGAACTTATCGAGCTTA
TTGGAAATGGACAGTTTAGCAAAGGCATGGATTGGCAGACTGTGTCTCTGGCAATTAATGAAGTCTTTAATGAACTTATA
CTAGATGTATTAAAACAGGGTTACATGATGAAAAAGGGCCACAGACTGAAAAACTGGACTGAACGATGGTCTGTACTAAA
ACGCAACATAATTTCTTACTATGTGAGTGAGGACCTGAATGATAAGAAAGGAGACATTCTCTTGGATGAAAACTGCTGTT
TAGAGTCCTTGCCTGACAAAGATGGAAAGAAATGCCTTTTTCTCGTAAAATGTTTTGATAAGACTTTTGAAATTGGTGCT
TCAGCTAAGAAGAAGAAACAGGAGTGGATAAAAGCCATTCATTCTACTATTCATCTGTTGAAGCTGGGCAGCCCTCCACC
ACACAAAGAAGCCTGACAGCGTCTGAAGGAACTCCGGAAGAAGCAACTGGCTGAACAAGAGGAAGTGGAGCGACAAATGA
AGGAGCTCCAGGCCGCCAACGAAAGCAGGCAGCTGGAGCTGGAGGCCGTGCGGAAGAAACAAGGAAGCAGCATCCCGTGC
AGCAGAAGAGGAAAAGAAACGCCTTCAGACTCAACTGGAACTTCAGGCCAGGTTCAGCACAGAGCTGGAAAGAAAGAAGC
TTATTAAACAGCAGATGGAAGGACAGGTTGCTCCAAAGTCCTCTGAACTGGGACAGTATTTACAGCGAGTACGGGAGCTG
GAAGACATGTACCTAAGGCTGCAAGAGGCTCTTGAGGATGAGAGACAGGCCCGGCAAGATGATGAGACGGTGCGGAAGCT
TCAGGCCAGGTTGTTGGAGGAAGAGTCTTCCAAGAGGGCTGAACTAGAAAAGTGGCACTTGGAGCAGCAGCAGGCCATTC
AGACGACTGAGACAGAGAAGCAGGAGTTGGAGAATCAGCGTGTCCTGGAGAAGCGGGCCCTGCAAGAAGCCATGGAGCAG
CTGGAGTTGGAACGGAAACAAGCACTTGAGCAGTACTAGGAAGTTAAAAAGAAGCTGGAGATGGCAACTAATAAGACCAA
GAGTTGGAAGGACGACGTGGCCCATCGTGAAGGATTAATTCAACTGATAGAACCAGGTTCAAAGAACCCTCACCTGATCA
CTAACTGGGGACCTGCTACTTTCGTTGAGGCAGAACTTGAAGAGAGAACTGGAAAGAGAAAAAGACCACGGAGT

Alignment

ORF - retro_cjac_1605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.27 %
• Parental protein coverage: 82.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKNLTK-NPLLITEEDAFKVWVIFNFLSEDKYPLIIVTEEIEYLLKKLTEAMGGGWQQEQFEHYKVNFDD
          KKNLTK.NPLLITE.DAFKVWVIFNF.SE.KYPLIIVTEEIEYLLKKLTEAMGGGWQQEQFEHYKVNFDD
Retrocopy KKNLTK>NPLLITEDDAFKVWVIFNFVSEAKYPLIIVTEEIEYLLKKLTEAMGGGWQQEQFEHYKVNFDD

Parental  SKDGLSAW-ELIELIGNGQFSKGMDRQTVSMAINEVFNELILDVLKQGYMMKKGHRRKNWTERWFVLKPN
          SKDG.....ELI...GNGQFSKGMD.QTVS.AINEVFNELILDVLKQGYMMKKGHR.KNWTERW.VLK.N
Retrocopy SKDGVGTY>ELI---GNGQFSKGMDWQTVSLAINEVFNELILDVLKQGYMMKKGHRLKNWTERWSVLKRN

Parental  IISYYVSEDLNDKKGDILLDENCCVESLPDKDGKKCLFLVKCFDKTFEISASDKKKKQEWIQAIHSTIHL
          IISYYVSEDLNDKKGDILLDENCC.ESLPDKDGKKCLFLVKCFDKTFEI.AS.KKKKQEWI.AIHSTIHL
Retrocopy IISYYVSEDLNDKKGDILLDENCCLESLPDKDGKKCLFLVKCFDKTFEIGASAKKKKQEWIKAIHSTIHL

Parental  LKLGSPPPHKEARQRRKELRKKQLAEQEELERQMKELQAANESKQLELEAVRKK-LEEAASRAAEEEKKR
          LKLGSPPPHKEA.QR.KELRKKQLAEQEE.ERQMKELQAANES.QLELEAVRKK..E.A...A.EEEKKR
Retrocopy LKLGSPPPHKEA*QRLKELRKKQLAEQEEVERQMKELQAANESRQLELEAVRKK>KEAASRAA-EEEKKR

Parental  LQTQVELQARFSTELEREKLIRQQMEEQVAQKSSELEQYLLRVRELEDMYLRLQEALEDERQARQDEETV
          LQTQ.ELQARFSTELER.KLI.QQME.QVA.KSSEL.QYL.RVRELEDMYLRLQEALEDERQARQD.ETV
Retrocopy LQTQLELQARFSTELERKKLIKQQMEGQVAPKSSELGQYLQRVRELEDMYLRLQEALEDERQARQDDETV

Parental  RKLQARLLEEESSKRAELEKWHLEQQQAIQMTEAEKQELENQRVLKEQALQEAMEQLEQLELERKQALEQ
          RKLQARLLEEESSKRAELEKWHLEQQQAIQ.TE.EKQELENQRVL...ALQEAMEQLE...LERKQALEQ
Retrocopy RKLQARLLEEESSKRAELEKWHLEQQQAIQTTETEKQELENQRVLEKRALQEAMEQLE---LERKQALEQ

Parental  YEEVKKKLEMATNKTKSWKDKVAHHEGLIRLIEPGSKNPHLITNWGPAAFTEAELEEREKNWKEKKT
          Y.EVKKKLEMATNKTKSWKD.VAH.EGLI.LIEPGSKNPHLITNWGPA.F.EAELEER....K....
Retrocopy Y*EVKKKLEMATNKTKSWKDDVAHREGLIQLIEPGSKNPHLITNWGPATFVEAELEERTGKRKRPRS

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	7.23 RPM
SRP051959_heart	0.02 RPM	20.84 RPM
SRP051959_kidney	0.00 RPM	8.16 RPM
SRP051959_liver	0.00 RPM	9.29 RPM
SRP051959_lung	0.03 RPM	14.71 RPM
SRP051959_lymph_node	0.00 RPM	13.72 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.21 RPM
SRP051959_spleen	0.04 RPM	30.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1605 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1605 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1605 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	ENSCJAG00000011252	1 retrocopy	retro_cjac_1605 ,
Callithrix jacchus	ENSCJAG00000015575	2 retrocopies	retro_cjac_10, retro_cjac_313,