RetrogeneDB ID: retro_cjac_1238

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:1054898..1055985(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPP40
• Ensembl ID: ENSCJAG00000021373
• Aliases: None
• Description: None

Sequence

>retro_cjac_1238
ATGGCCACGCTGCGCCGGCTTCGGGAGGTTCCGCGGTACTTACTGGTTTGCGAGAAATCCAACTTGGGCAACCACAAGTC
GCGCCACCGGCATGTCGTTCAGACGCGCTGTTATAACTACAGGGTTTTATTTCTCATTCCCGAATGTGGGATACTATTGG
AAGAACTGAAAAACCTGGTCATGCAAACTGGACCCTATTATTTTGTGAAGAATTTACTCTTCATGAATTAATCACACACC
AATTCATTAGTACCTTTATAAAGAAAGGTTCTTGCTGTGCACTAACATATAATACAAATATTGATGAAGATAATACTGTT
GCCCTGCTACTAAATGGGACATTAATTTTGTCATTGGATAAAGACACTTACGAAGAAACTGGACTTCAGGGTTGTCCATC
TCAGTTTTCTGGCAGAAAAATTATGAAATTTATTGTTTCCATTGACTTGATGGTAATATCTTTAATCTTGGATTCTAAGA
AGTATGAAATAATATCTTTGTCCTTCAAAGAAAAGAAGCCATTGAAATTTGATTTTCTTTTGGCTTGGCATAATACGGGG
TCAAAAGAGTCAACAATGATGTCATACTCTTCCAAGTACCAAATTCAGGAGCATCAGCCAAAAGTGGCACTGAGCACATT
GAGAGATCTCCAGTGCCCAGTGCTGCAGAGCAGCAATCTCGAGGGAATGCTGGACGTGTCCTGCCGGGTGCTGGAGCTCT
TCGACTGGCTTGGTGCCATCTTCAGTAATGTCAACCTAAATAATGAGCCTAATAATTTCATATCAACCTATTGCTGCCCT
CAACCAAACACAGTGGTGGCAAAAGCTTATTTGTGTACAATCACTGGCTTCATACTTCCAGAGAAGATCTGTCTCCTACT
GGATCATCTCTGTCACTACTATGATGAATCAAAATTAGCTCCGTGGGTTACATTGTCTGTTCAAGGCGTTGCAGACAGCC
CTGTTTCTTGGGGAAAAAATTAACATGGTTTTCGAAAAGGAGGAGAACATTTATACAACTTTGTGATTTTAATAATTAGG
ACTACTGGCTTCAGATGGCTGTTGGGGCAAATGATCACTGTCCACCC

Alignment

ORF - retro_cjac_1238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATLRRLREVPRHLLVCEKSNFGNHKSRHRHIIQTHYYNYRVSFLIPECGILSEELKNLVMQTGPYYFVK
          MATLRRLREVPR.LLVCEKSN.GNHKSRHRH..QT..YNYRV.FLIPECGIL.EELKNLVMQTGPYYFVK
Retrocopy MATLRRLREVPRYLLVCEKSNLGNHKSRHRHVVQTRCYNYRVLFLIPECGILLEELKNLVMQTGPYYFVK

Parental  NL-PLHELITHEFISTFIKKGSCCALTYNTNIDEDNTVALLPNGTLILSLDKDTYEETGLQGRPSQFSGR
          NL..LHELITH.FISTFIKKGSCCALTYNTNIDEDNTVALL.NGTLILSLDKDTYEETGLQG.PSQFSGR
Retrocopy NL<TLHELITHQFISTFIKKGSCCALTYNTNIDEDNTVALLLNGTLILSLDKDTYEETGLQGCPSQFSGR

Parental  KIMKFIVSIDLMELSLNLDSKKYERISWSFKEKKPLKFDFLLAWHNAGSEESTMMSYFSKYQIQEHQPKV
          KIMKFIVSIDLM..SL.LDSKKYE.IS.SFKEKKPLKFDFLLAWHN.GS.ESTMMSY.SKYQIQEHQPKV
Retrocopy KIMKFIVSIDLMVISLILDSKKYEIISLSFKEKKPLKFDFLLAWHNTGSKESTMMSYSSKYQIQEHQPKV

Parental  ALSTLRDLQCPVLQSSELEGTPDVSCRALELFDWLGAVFSNVDLNNESNNFISTYCCPQPSTVVAKAYLC
          ALSTLRDLQCPVLQSS.LEG..DVSCR.LELFDWLGA.FSNV.LNNE.NNFISTYCCPQP.TVVAKAYLC
Retrocopy ALSTLRDLQCPVLQSSNLEGMLDVSCRVLELFDWLGAIFSNVNLNNEPNNFISTYCCPQPNTVVAKAYLC

Parental  TITGFILPEKICLLLERLCHYYDEPKLAPWVTLSVQGFADSPVSWGKNEHGFRKGGEHLYNFVI-FNNQD
          TITGFILPEKICLLL..LCHYYDE.KLAPWVTLSVQG.ADSPVSWGKN.HGFRKGGEHLYNFVI.FNN.D
Retrocopy TITGFILPEKICLLLDHLCHYYDESKLAPWVTLSVQGVADSPVSWGKN*HGFRKGGEHLYNFVI<FNN*D

Parental  YWLQMAVGANDHCPP
          YWLQMAVGANDHCPP
Retrocopy YWLQMAVGANDHCPP

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	1.89 RPM
SRP051959_heart	0.00 RPM	1.26 RPM
SRP051959_kidney	0.00 RPM	2.13 RPM
SRP051959_liver	0.00 RPM	3.66 RPM
SRP051959_lung	0.00 RPM	1.74 RPM
SRP051959_lymph_node	0.00 RPM	1.64 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.23 RPM
SRP051959_spleen	0.00 RPM	2.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1238 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1238 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	ENSCJAG00000021373	1 retrocopy	retro_cjac_1238 ,