RetrogeneDB ID: retro_cjac_601

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:108233850..108235532(-)
• Located in intron of: ENSCJAG00000011661

Retrocopy information

• Ensembl ID: ENSCJAG00000011742
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPN1
• Ensembl ID: ENSCJAG00000017529
• Aliases: None
• Description: ribophorin I [Source:HGNC Symbol;Acc:10381]

Sequence

>retro_cjac_601
TCTAAGGTGACAGCGGAGGTGGTCCTGGCGCACCTGGGCAGTGGCTCCACGTCCTGAGCTACCTCTTTCCTTCTGCTTTG
GAGCCCAACCTCGAGGCTCGGCTGGTGCATCTGGGCGTGCAGGTGAAGGGAGAAGATGAGGAAGAGAACAATTTGGAAGT
ACGGGAAACCAAAATTAAGGTTAAAAGTGGGAAATTCTTCACAGTCAAGCTCCCACTTGCTCTTGATCCTGGGGCCAAGA
TTTCAGTCATTGTGGAGACAGTCTACACCCATGTGCTTCAGCCATATCCAACTCAGATCACTCAGTCAGAGAAACAGTTT
GTGGTGTTTGAGGGGAACCATTATTTCTACTCTCCCTATCCAACAAAGAGACAAACCATGCATGTGAAGCTTGCCTCCCG
AAATGTGGAGAGCTACACCAAGCTGGGGAACCCCATGCGCCCCGAGGAACTGCTGGATTATGGGCCGTTCAGAGATGTCC
CTGCCTATAGTCAGGATACTTTTAAAGTACATTATGAGAACAACAGTCCTTTCCTGACCATCACCAGCATGTCTAGAGTC
ATTGAAGTCTCTCACTGGGGTAATATTGCTGTGGAAGAAAATGTGGACTTGAAGCACACAGGGGCTGTGCTTAAGGGGCC
TTTCTCATGCTATGATTACCAGAGACAGCCAGATAGTGGAATATCCTCCATCAGTTCTTTTAAGACCATCCTTCCTGCTG
CTGCCCAGGATGTTTATTACTGGGATGAGATTGGCAATGTTTCCACCAGTCACCTCCTTATTTTGGATGACTCTGTAGAG
GTGGAAATCTGGCCTCGCTTCCCTCTCTTTGGCAGGTGGAAGACCCATTACACCATTGGCTACAACCTTCCAAGCTGTGA
GTACCTCTATAATTTGGGTGACCAGTATGCACTGAAGATGAGGTTTGTCGACTATGTGTTTGATGAACAAGTGATAGATT
CTCTGACTGTGAAGATCATCCTGCCTGAAGGAGCGAAGAACATTGAAATTGATAGTCCCTATGAAATCAGCCGTTCCCCA
GATGAGCTGCACTACACCTATCTGGATACGTTCGGCCGCCCTGTGATTGTTGCCTACAAGAAAAATCTGGTAGAACAGCA
CATTCAGGACATTGTGGTCCACTACACATTCAACAAGGTGCTTAGGCTGCAGGAGCCCCTGCTCGTGGTGGCAGCCTTCT
ACATCCTGTTCTTCACTGTCATAATCTATGTCCAGCTGGACTTCTCCATCACCAAGGATCCGGCCACAGAAGCCAGGATG
AGGGTAGCCTGCATCACAGAGCAGGTCTTGACCCTGGTCAACAAGCGAACAGGCCTTTACCGTCACTTTGATGAGACTGT
CAACAGGTATAAGCAATCCCAGGACATCTCCACCCTCAACAGTGGCAAGAAGAGCCTGGAGACTGAACACAAGGCCTTGA
CCAGTGAGATTGCACTGCTGCAGTCCAGGCTGAAGACAGATGGCTCTGATCTGGGTGACAGAGTAAGCGAAATGCAGAAG
CTGGATGCACAGGTCAAGGAGCTGGTGCTGAAGTCAGCGGTGGAGGCTGAGCTCCTGGTGGCTGGCAAGCTCAAGAAAGA
CACATACATTGAGAATGAGAAGCTCATCTCAGGAAAGCGCCAGGAGCTGGTCACCAAGATCGACCACATCCTGGATGCCC
TG

Alignment

ORF - retro_cjac_601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.95 %
• Parental protein coverage: 92.42 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKVTAEVVLAHLGSSSTSRATSFLL-ALEPDLEVRLAHLGVQVKGEDEEENNLEVRETKIKGKSGKFFTV
          .KVTAEVVLAHLGS.STS.ATSFLL.ALEP.LE.RL.HLGVQVKGEDEEENNLEVRETKIK.KSGKFFTV
Retrocopy SKVTAEVVLAHLGSGSTS*ATSFLL<ALEPNLEARLVHLGVQVKGEDEEENNLEVRETKIKVKSGKFFTV

Parental  KLPVALDPGAKISVIVETVYTHVLQPYPTQITQSEKQFVVFEGNHYFYSPYPTKTQTMRVKLASRNVESY
          KLP.ALDPGAKISVIVETVYTHVLQPYPTQITQSEKQFVVFEGNHYFYSPYPTK.QTM.VKLASRNVESY
Retrocopy KLPLALDPGAKISVIVETVYTHVLQPYPTQITQSEKQFVVFEGNHYFYSPYPTKRQTMHVKLASRNVESY

Parental  TKLGNPTRSEDLLDYGPFRDVPAYSQDTFKVHYENNSPFLTITSMTRVIEVSHWGNIAVEENVDLKHTGA
          TKLGNP.R.E.LLDYGPFRDVPAYSQDTFKVHYENNSPFLTITSM.RVIEVSHWGNIAVEENVDLKHTGA
Retrocopy TKLGNPMRPEELLDYGPFRDVPAYSQDTFKVHYENNSPFLTITSMSRVIEVSHWGNIAVEENVDLKHTGA

Parental  VLKGPFSRYDYQRQPDSGISSIRSFKTILPAAAQDVYYRDEIGNVSTSHLLILDDSVEMEIRPRFPLFGG
          VLKGPFS.YDYQRQPDSGISSI.SFKTILPAAAQDVYY.DEIGNVSTSHLLILDDSVE.EI.PRFPLFG.
Retrocopy VLKGPFSCYDYQRQPDSGISSISSFKTILPAAAQDVYYWDEIGNVSTSHLLILDDSVEVEIWPRFPLFGR

Parental  WKTHYIVGYNLPSYEYLYNLGDQYALKMRFVDHVFDEQVIDSLTVKIILPEGAKNIEIDSPYEISRSPDE
          WKTHY..GYNLPS.EYLYNLGDQYALKMRFVD.VFDEQVIDSLTVKIILPEGAKNIEIDSPYEISRSPDE
Retrocopy WKTHYTIGYNLPSCEYLYNLGDQYALKMRFVDYVFDEQVIDSLTVKIILPEGAKNIEIDSPYEISRSPDE

Parental  LHYTYLDTFGRPVIVAYKKNLVEQHIQDIVVHYTFNKVLMLQEPLLVVAAFYILFFTVIIYVRLDFSITK
          LHYTYLDTFGRPVIVAYKKNLVEQHIQDIVVHYTFNKVL.LQEPLLVVAAFYILFFTVIIYV.LDFSITK
Retrocopy LHYTYLDTFGRPVIVAYKKNLVEQHIQDIVVHYTFNKVLRLQEPLLVVAAFYILFFTVIIYVQLDFSITK

Parental  DPAAEARMKVACITEQVLTLVNKRIGLYRHFDETVNRYKQSRDISTLNSGKKSLETEHKALTSEIALLQS
          DPA.EARM.VACITEQVLTLVNKR.GLYRHFDETVNRYKQS.DISTLNSGKKSLETEHKALTSEIALLQS
Retrocopy DPATEARMRVACITEQVLTLVNKRTGLYRHFDETVNRYKQSQDISTLNSGKKSLETEHKALTSEIALLQS

Parental  RLKTEGSDLCDRVSEMQKLDAQVKELVLKSAVEAERLVAGKLKKDTYIENEKLISGKRQELVTKIDHILD
          RLKT.GSDL.DRVSEMQKLDAQVKELVLKSAVEAE.LVAGKLKKDTYIENEKLISGKRQELVTKIDHILD
Retrocopy RLKTDGSDLGDRVSEMQKLDAQVKELVLKSAVEAELLVAGKLKKDTYIENEKLISGKRQELVTKIDHILD

Parental  AL
          AL
Retrocopy AL

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	0.20 RPM	89.97 RPM
SRP051959_heart	0.05 RPM	49.76 RPM
SRP051959_kidney	0.44 RPM	102.34 RPM
SRP051959_liver	3.40 RPM	152.60 RPM
SRP051959_lung	0.33 RPM	82.39 RPM
SRP051959_lymph_node	0.32 RPM	83.42 RPM
SRP051959_skeletal_muscle	0.04 RPM	50.45 RPM
SRP051959_spleen	0.76 RPM	96.22 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_601 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_601 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005191	1 retrocopy	retro_btau_123,
Callithrix jacchus	ENSCJAG00000017529	1 retrocopy	retro_cjac_601 ,
Myotis lucifugus	ENSMLUG00000017213	1 retrocopy	retro_mluc_721,
Oryctolagus cuniculus	ENSOCUG00000011098	1 retrocopy	retro_ocun_899,