RetrogeneDB ID: retro_cjac_2987

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:70612835..70613175(-)
• Located in intron of: ENSCJAG00000001754

Retrocopy information

• Ensembl ID: ENSCJAG00000001784
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TCEB2
• Ensembl ID: ENSCJAG00000015347
• Aliases: None
• Description: transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B) [Source:HGNC Symbol;Acc:11619]

Sequence

>retro_cjac_2987
GATATGGTTCCTCATGTCCAGTGCCACAAGACCACCATCTTCACAGATGCCAAGGCATCCAGCATCACGTTTGAGGTGAA
GCGCATCATCAAGGGCATTCCCAAGCAGCCGCCCGATGAGCAGCAGCTGTACAAGAACGACCAACTCTCGGATGATAGTA
AGACATTGGGTGAGTGTGGCTTCACCTGTCAAAAGCGCGGCCACAGCCCTCAGCCAGAGTGGGGCTGGCCTTCCAGGCAG
ATGACACCTTTGAGGCCCTGTGCATCGAGCCGTTCTCCGGTCCGCCAGAGCTGCCCGATGTGATGAAGCCCAGGACTCCA
GAAGCAGTGCCAATGAAAAA

Alignment

ORF - retro_cjac_2987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.28 %
• Parental protein coverage: 96.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQ-TARPQ
          D.......HKTTIFTDAK.SS..FE.KRI..GI.K.PPDEQ.LYK.DQL.DD.KTLGECGFT.Q..ARPQ
Retrocopy DMVPHVQCHKTTIFTDAKASSITFEVKRIIKGIPKQPPDEQQLYKNDQLSDDSKTLGECGFTCQ<KARPQ

Parental  APATVGLAFRAEDTFEALCIEPFSSPPELPDVMKP-QDSGSSANEQ
          ..A.VGLAF.A.DTFEALCIEPFS.PPELPDVMKP.QDS.SSANE.
Retrocopy PSARVGLAFQADDTFEALCIEPFSGPPELPDVMKP<QDSRSSANEK

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	0.11 RPM	10.29 RPM
SRP051959_heart	0.07 RPM	12.87 RPM
SRP051959_kidney	0.02 RPM	13.42 RPM
SRP051959_liver	0.09 RPM	16.83 RPM
SRP051959_lung	0.10 RPM	8.82 RPM
SRP051959_lymph_node	0.07 RPM	7.35 RPM
SRP051959_skeletal_muscle	0.07 RPM	24.09 RPM
SRP051959_spleen	0.04 RPM	7.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2987 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2987 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019543	3 retrocopies	retro_btau_142, retro_btau_17, retro_btau_29,
Callithrix jacchus	ENSCJAG00000015347	10 retrocopies	retro_cjac_1593, retro_cjac_1606, retro_cjac_2051, retro_cjac_2613, retro_cjac_2987 , retro_cjac_3030, retro_cjac_342, retro_cjac_3819, retro_cjac_639, retro_cjac_959,
Cavia porcellus	ENSCPOG00000021024	1 retrocopy	retro_cpor_1416,
Felis catus	ENSFCAG00000004711	2 retrocopies	retro_fcat_112, retro_fcat_40,
Homo sapiens	ENSG00000103363	2 retrocopies	retro_hsap_1246, retro_hsap_940,
Gorilla gorilla	ENSGGOG00000015306	1 retrocopy	retro_ggor_976,
Monodelphis domestica	ENSMODG00000016536	4 retrocopies	retro_mdom_1149, retro_mdom_1617, retro_mdom_1964, retro_mdom_23,
Mustela putorius furo	ENSMPUG00000015265	1 retrocopy	retro_mputfur_469,
Mus musculus	ENSMUSG00000055839	7 retrocopies	retro_mmus_1212, retro_mmus_1489, retro_mmus_1664, retro_mmus_2930, retro_mmus_511, retro_mmus_747, retro_mmus_99,
Nomascus leucogenys	ENSNLEG00000009471	2 retrocopies	retro_nleu_295, retro_nleu_89,
Oryctolagus cuniculus	ENSOCUG00000010116	2 retrocopies	retro_ocun_202, retro_ocun_930,
Pongo abelii	ENSPPYG00000007013	1 retrocopy	retro_pabe_74,
Pan troglodytes	ENSPTRG00000007663	1 retrocopy	retro_ptro_857,
Rattus norvegicus	ENSRNOG00000004814	6 retrocopies	retro_rnor_1226, retro_rnor_1275, retro_rnor_185, retro_rnor_1948, retro_rnor_35, retro_rnor_352,
Sus scrofa	ENSSSCG00000008061	1 retrocopy	retro_sscr_858,
Tursiops truncatus	ENSTTRG00000015454	5 retrocopies	retro_ttru_1030, retro_ttru_109, retro_ttru_1276, retro_ttru_1909, retro_ttru_273,