RetrogeneDB ID: retro_cjac_162

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:17561601..17562138(-)
• Located in intron of: ENSCJAG00000012743

Retrocopy information

• Ensembl ID: ENSCJAG00000023047
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005359
• Aliases: None
• Description: None

Sequence

>retro_cjac_162
ATGTCGAGTTTCTCCAGGACTCCCCAGCAATGGGCCACTTTTGCTAGAGTATGGTATCTCTTAGATGGGAAAATGCAGCC
ACCTGGCAAACTTGCCTCTATGGCATCAATAAGACTTCAGGGATTACATAAACCTGTGTACCATGAACTTAGTGACTGTG
GGGATCATGTTGTTATAATGAACACAAGACACATTGCATTTTCTGGAAACAAATGGGAACAAAAAGTATACTCCTCCCAC
ACTGGCTACCCAGGTGGAGTTAGACAAGTAACAGCTGCTCAGCTTCACCTGAAGGATCCAGTGGCAATTGTAAAACTAGC
TATTTATGGCATGCTACCAAAAAACCTTCACAGAAGAACAATGATGCAAAGGTTGCATCTTTTCCCAGATGAGGATATTC
CAGAAGATATTCTTAAGAATTTAGTGGAAGAGCTTCCACAACCACGAAAAATACCTAAACGTCTGGATGAGTACACACAA
GAAGAAATAGACGCTTTCCCAAGATTGTGGACTCCACCTGAAGATTTTCGGCTATAA

Alignment

ORF - retro_cjac_162 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSFSRTPQQWATFARVWYLLDGKMQPPGKLASMASIRLQGLHKPVYHELSDCGDHVVIMNTRHIAFSGN
          MSSFSRTPQQWATFARVWYLLDGKMQPPGKLASMASIRLQGLHKPVYHELSDCGDHVVIMNTRHIAFSGN
Retrocopy MSSFSRTPQQWATFARVWYLLDGKMQPPGKLASMASIRLQGLHKPVYHELSDCGDHVVIMNTRHIAFSGN

Parental  KWEQKVYSSHTGYPGGFRQVTAAQLHLKDPVAIVKLAIYGMLPKNLHRRTMMQRLHLFPDEDIPEDILKN
          KWEQKVYSSHTGYPGG.RQVTAAQLHLKDPVAIVKLAIYGMLPKNLHRRTMMQRLHLFPDEDIPEDILKN
Retrocopy KWEQKVYSSHTGYPGGVRQVTAAQLHLKDPVAIVKLAIYGMLPKNLHRRTMMQRLHLFPDEDIPEDILKN

Parental  LVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDFRL
          LVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDFRL
Retrocopy LVEELPQPRKIPKRLDEYTQEEIDAFPRLWTPPEDFRL

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	0.13 RPM	4.26 RPM
SRP051959_heart	0.02 RPM	4.68 RPM
SRP051959_kidney	0.09 RPM	6.19 RPM
SRP051959_liver	0.02 RPM	6.89 RPM
SRP051959_lung	0.10 RPM	4.41 RPM
SRP051959_lymph_node	0.14 RPM	3.81 RPM
SRP051959_skeletal_muscle	0.13 RPM	5.74 RPM
SRP051959_spleen	0.11 RPM	4.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_162 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_162 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_162 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006926	1 retrocopy	retro_chof_648,
Callithrix jacchus	ENSCJAG00000005359	1 retrocopy	retro_cjac_162 ,
Dipodomys ordii	ENSDORG00000016654	1 retrocopy	retro_dord_480,
Equus caballus	ENSECAG00000021161	1 retrocopy	retro_ecab_952,
Mustela putorius furo	ENSMPUG00000001080	2 retrocopies	retro_mputfur_1585, retro_mputfur_623,
Oryctolagus cuniculus	ENSOCUG00000016189	1 retrocopy	retro_ocun_675,
Ochotona princeps	ENSOPRG00000015721	2 retrocopies	retro_opri_274, retro_opri_454,
Pteropus vampyrus	ENSPVAG00000003719	1 retrocopy	retro_pvam_627,
Rattus norvegicus	ENSRNOG00000004401	1 retrocopy	retro_rnor_2720,
Sus scrofa	ENSSSCG00000005996	1 retrocopy	retro_sscr_1183,
Tupaia belangeri	ENSTBEG00000004571	5 retrocopies	retro_tbel_1026, retro_tbel_1596, retro_tbel_2517, retro_tbel_3095, retro_tbel_456,