RetrogeneDB ID: retro_cjac_1022

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:31256901..31257903(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMS2
• Ensembl ID: ENSCJAG00000010803
• Aliases: None
• Description: None

Sequence

>retro_cjac_1022
ATGCTGCTATCCGTGACTTCCAGGCCTGGGATTTCGACTTTGGGCTACAGTAGAAACAACAAGAAGCCATATGTGTCATT
GGCTCAGCAGATGGCACCACCTAGCCCAAGCAACAGTACCCCTAACAGCAGCAGTGGAAGCAATGGAAATGACCAGCTGA
GCAAAACCAACCTATACATCCGAGGATTGCAACCAGGCACTACTGACCAAGATCTTGTCAAGCTGTGTCAGCCATATGGC
AAGATTGTCTCCACTAAGGCCATACTGGACAAGACCACAAACAAATGCAAAGGCTATGGCTTTGTAGATTTTGACAGCCC
TTCAGCAGCACAGAAAGCTGTAACAGCACTGAAGGCCAGTGGGGTACAGGCACAGATGGCAAAGCAACAGGAACAGGACC
CCCCAAATTTATACATCTCTAACCTCCCACTGTCAATGGATGAGCAGGAACTGGAGGGGATGCTGAAGCCCTTTGGCCAG
GTTATCTCCACCTGTATCCTTCGAGACACCAGTGGGACCAGCAGAGGGGTTGGCTTTGCAAAGATGGAGTCCACAGAGAA
GTGTAAAGCCATCATCACCCACTTTAATGGAAAATATATTAAGACACCCCCTGGAGTACCGGCCCCATCCAATCCCTTGC
TTTGCAAATTTGCTGATGGCGGGCCAAAGAAACGACAGAACCAAGGAAAATTTGTGCAAAATGGACAGGCCTGGCTAAGG
AATGGAGACATGGGTAGCATGGCCTTGACCTATGACCCCACCACGTCTCTTCAGAATGGGTTTTACCCTTATAACATCAC
CCCCAACAGGATGCTTGCTCAGTCTGCATTCTCCCCATACCTTTCCTCTCCTGTGTCTTCGTATCAGAGAGTGACTCAGA
CATCTCCTCTAAAAGTACCTAACCCATCTTGGATGCACCACCATTCATACCTCATGCAACCTTCAGGTTCAGTTCTGACA
CCAGGGATGGACCATCCTATTTCTCTCCAGCCAGCCTCCATC

Alignment

ORF - retro_cjac_1022 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.13 %
• Parental protein coverage: 82.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLSVTSRPGISTLGYSRNNKKPYVSLAQQMAPPSPSNSTPNSSSGSNGNDQLSKTNLYIRGLQPGTTDQ
          MLLSVTSRPGISTLGYSRNNKKPYVSLAQQMAPPSPSNSTPNSSSGSNGNDQLSKTNLYIRGLQPGTTDQ
Retrocopy MLLSVTSRPGISTLGYSRNNKKPYVSLAQQMAPPSPSNSTPNSSSGSNGNDQLSKTNLYIRGLQPGTTDQ

Parental  DLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQQEQDPTNLYIS
          DLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQQEQDP.NLYIS
Retrocopy DLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQQEQDPPNLYIS

Parental  NLPLSMDEQELEGMLKPFGQVISTRILRDTSGTSRGVGFARMESTEKCEAIITHFNGKYIKTPPGVPAPS
          NLPLSMDEQELEGMLKPFGQVIST.ILRDTSGTSRGVGFA.MESTEKC.AIITHFNGKYIKTPPGVPAPS
Retrocopy NLPLSMDEQELEGMLKPFGQVISTCILRDTSGTSRGVGFAKMESTEKCKAIITHFNGKYIKTPPGVPAPS

Parental  DPLLCKFADGGPKKRQNQGKFVQNGRAWPRNGDMGSMALTYDPTTSLQNGFYPAPYNITPNRMLAQSALS
          .PLLCKFADGGPKKRQNQGKFVQNG.AW.RNGDMGSMALTYDPTTSLQNGFY..PYNITPNRMLAQSA.S
Retrocopy NPLLCKFADGGPKKRQNQGKFVQNGQAWLRNGDMGSMALTYDPTTSLQNGFY--PYNITPNRMLAQSAFS

Parental  PYLSSSVSSYQRVTQTSPLQVPNPSWMHHHSYLMQPSGSVLTPGMDHPISLQPASM
          PYLSS.VSSYQRVTQTSPL.VPNPSWMHHHSYLMQPSGSVLTPGMDHPISLQPAS.
Retrocopy PYLSSPVSSYQRVTQTSPLKVPNPSWMHHHSYLMQPSGSVLTPGMDHPISLQPASI

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	0.33 RPM	8.74 RPM
SRP051959_heart	0.49 RPM	15.38 RPM
SRP051959_kidney	0.64 RPM	9.12 RPM
SRP051959_liver	0.22 RPM	3.40 RPM
SRP051959_lung	1.43 RPM	35.41 RPM
SRP051959_lymph_node	0.21 RPM	6.05 RPM
SRP051959_skeletal_muscle	0.39 RPM	5.70 RPM
SRP051959_spleen	0.57 RPM	14.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1022 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1022 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004054	1 retrocopy	retro_amel_454,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Callithrix jacchus	ENSCJAG00000010803	1 retrocopy	retro_cjac_1022 ,
Callithrix jacchus	ENSCJAG00000014861	1 retrocopy	retro_cjac_1040,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000076067	1 retrocopy	retro_hsap_1143,
Myotis lucifugus	ENSMLUG00000000530	1 retrocopy	retro_mluc_1093,
Mus musculus	ENSMUSG00000040043	1 retrocopy	retro_mmus_1530,
Pan troglodytes	ENSPTRG00000005104	1 retrocopy	retro_ptro_778,
Pteropus vampyrus	ENSPVAG00000007616	2 retrocopies	retro_pvam_1429, retro_pvam_695,
Rattus norvegicus	ENSRNOG00000003076	1 retrocopy	retro_rnor_1374,
Sus scrofa	ENSSSCG00000000402	1 retrocopy	retro_sscr_546,
Tursiops truncatus	ENSTTRG00000002117	1 retrocopy	retro_ttru_715,