RetrogeneDB ID: retro_cjac_2325

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:33078620..33079357(+)
• Located in intron of: ENSCJAG00000001638

Retrocopy information

• Ensembl ID: ENSCJAG00000001682
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSCJAG00000020875
• Aliases: None
• Description: None

Sequence

>retro_cjac_2325
ATGGCTGAAGAGCTCTCCGTGGCCACTTCCTGCACCGAAGATGATTTCTACTGCCCAGTCTGTCTAGGAGGTGCTCAAAA
CGCCCGTGCGGACTGTGGCCCATCAGCACGTTTTCTGTAGAAAATGTTTCCTGACTGCAATGAGGGAAAGAGGAGCACAT
TGTCCCTTGTGTCGTGGAAATGTGACTAGAAGAGAGAGAGCATGTCCCCAACAGGCTTTAGACCCTGAAAATATCATGAG
GAAGTTTTATGGTAGCTGCAGATGCTGTGCAAAACAGATTAAATTCTATCGCATGAGACATCATTACAAATCTTGTAAGA
AGTATCAGGATGAATATGGTGTTTTTTTCTACCATTCCAAACTTTCAGATCTCTCAAGATTCAGTAGGGAACAGTAATAG
GAGTGAAACATCCACATCTGATAACACAGAACCTTACCAAGAGAATACAAGTTCTTCTGGTCATCCCATTTTTAAGTGTC
CCCTGTGTCAAGAATCAAATTTTACCAGGCAGCGTTTACTGGATCACTGTAACAGTAATCACCTATTTCAGATAATTCCT
GTGACATGTCCCATTTGTGTGTCTCTTCCTTGGGGAGATCCTCACCAGATAACTAGAAATTTTGTTAGTCACCTAAATCA
GAGACATCAGTTTGATTACGGAGAGTTTGTGAATCTTCAGCTAGATGAAGAAACCCAGTATCAAACTGCTGTTGAAGAAT
CTTTTCAAGTAAACATC

Alignment

ORF - retro_cjac_2325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEELSAATSYTEDDFYCPVCQ-EVLKTPVRTAACQHVFCRKCFLTAMRESGAHCPLCRGNVTRRERACP
          MAEELS.ATS.TEDDFYCPVC..EVLKTPVRT.A.QHVFCRKCFLTAMRE.GAHCPLCRGNVTRRERACP
Retrocopy MAEELSVATSCTEDDFYCPVCL>EVLKTPVRTVAHQHVFCRKCFLTAMRERGAHCPLCRGNVTRRERACP

Parental  ERALDLENIMRKFSGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVS-SIIPNFQISQDSVGNSNRSETST
          ..ALD.ENIMRKF.GSCRCCAKQIKFYRMRHHYKSCKKYQDEYGV..S.IPNFQISQDSVGNSNRSETST
Retrocopy QQALDPENIMRKFYGSCRCCAKQIKFYRMRHHYKSCKKYQDEYGVF>STIPNFQISQDSVGNSNRSETST

Parental  SDNTETYQENTSSSGHPTFKCPLCQESNFTRQRLLDHCNSNHLFQIIPVTCPICVSLPWGDPRQITRNFV
          SDNTE.YQENTSSSGHP.FKCPLCQESNFTRQRLLDHCNSNHLFQIIPVTCPICVSLPWGDP.QITRNFV
Retrocopy SDNTEPYQENTSSSGHPIFKCPLCQESNFTRQRLLDHCNSNHLFQIIPVTCPICVSLPWGDPHQITRNFV

Parental  SHLNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI
          SHLNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI
Retrocopy SHLNQRHQFDYGEFVNLQLDEETQYQTAVEESFQVNI

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	0.73 RPM	13.05 RPM
SRP051959_heart	0.28 RPM	6.52 RPM
SRP051959_kidney	0.33 RPM	7.52 RPM
SRP051959_liver	0.37 RPM	9.05 RPM
SRP051959_lung	0.36 RPM	10.64 RPM
SRP051959_lymph_node	0.57 RPM	17.42 RPM
SRP051959_skeletal_muscle	0.13 RPM	2.64 RPM
SRP051959_spleen	0.53 RPM	15.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2325 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2325 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020160	1 retrocopy	retro_btau_322,
Choloepus hoffmanni	ENSCHOG00000012689	6 retrocopies	retro_chof_1043, retro_chof_1242, retro_chof_1931, retro_chof_418, retro_chof_714, retro_chof_793,
Callithrix jacchus	ENSCJAG00000020875	1 retrocopy	retro_cjac_2325 ,
Felis catus	ENSFCAG00000014180	2 retrocopies	retro_fcat_1383, retro_fcat_379,
Homo sapiens	ENSG00000134758	1 retrocopy	retro_hsap_3319,
Gorilla gorilla	ENSGGOG00000027857	1 retrocopy	retro_ggor_1302,
Loxodonta africana	ENSLAFG00000003811	1 retrocopy	retro_lafr_408,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mustela putorius furo	ENSMPUG00000006982	1 retrocopy	retro_mputfur_276,
Nomascus leucogenys	ENSNLEG00000006401	1 retrocopy	retro_nleu_1665,
Pongo abelii	ENSPPYG00000009094	1 retrocopy	retro_pabe_2734,
Pan troglodytes	ENSPTRG00000009956	1 retrocopy	retro_ptro_2155,
Pteropus vampyrus	ENSPVAG00000003778	2 retrocopies	retro_pvam_1316, retro_pvam_1379,
Rattus norvegicus	ENSRNOG00000015645	3 retrocopies	retro_rnor_2316, retro_rnor_808, retro_rnor_965,
Ictidomys tridecemlineatus	ENSSTOG00000002293	2 retrocopies	retro_itri_1443, retro_itri_576,