RetrogeneDB ID: retro_cjac_2095

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:16421275..16421753(-)
• Located in intron of: ENSCJAG00000013755

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA1
• Ensembl ID: ENSCJAG00000014407
• Aliases: None
• Description: transcription elongation factor A (SII), 1 [Source:HGNC Symbol;Acc:11612]

Sequence

>retro_cjac_2095
GCTGGAGCATTGGATTTGCTAAAGGAGCTTAAGAGTATTCCTATGACCCTGGAATTACCGCAGTCCACAAGAATCGGAAT
GTCATAAATGCTATTTGCAAGCAGAGTACAGATGAAGAAGTTACATCTTTGGCAAAGTCTCTCATCAAATCCTGGAAAAA
GTTATTAGATGGGCCATCAACTGAGAAAGACCTTGACGAAAAGAAAAAAGAACCTGCAATTACATCACAGAACAGCCCCG
ACGCAAGAGAAGAAAGTACCTCCAGCGCAATGTAAGCAACAGAAAGCATGAGAGAAATACTCGAGATGCTTAGGTTTCAT
CCTTTCCTCGGGCACCCAGCACTTCTGATTCTGTGCGGTTGAAGTGTAGGGAGACGCTTGCTGCAGCTCTTCAAACGGGA
GATGACTACATTGCAATTGGAGCTGATGAGGAAGAATTAGGATCTCAAATTGAAGAAGCTACATATCAAGAACTAAGG

Alignment

ORF - retro_cjac_2095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.12 %
• Parental protein coverage: 53.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AGALDLLKELKNIPMTLELLQSTRIGMS-VNAIRKQSTDEEVTSLAKSLIKSWKKLLDGPSTEKDLDEKK
          AGALDLLKELK.IPMTLEL.QSTRIGMS..NAI.KQSTDEEVTSLAKSLIKSWKKLLDGPSTEKDLDEKK
Retrocopy AGALDLLKELKSIPMTLELPQSTRIGMS<INAICKQSTDEEVTSLAKSLIKSWKKLLDGPSTEKDLDEKK

Parental  KEPAITSQNSPEAREESTSSG-NVSNRKDERNARDTYVSSFPRAPSTSDSVRLKCREMLAAALRTGDDYI
          KEPAITSQNSP.AREESTSS..NVSNRK.ERN.RD..VSSFPRAPSTSDSVRLKCRE.LAAAL.TGDDYI
Retrocopy KEPAITSQNSPDAREESTSSA<NVSNRKHERNTRDA*VSSFPRAPSTSDSVRLKCRETLAAALQTGDDYI

Parental  AIGADEEELGSQIEEAIYQEIR
          AIGADEEELGSQIEEA.YQE.R
Retrocopy AIGADEEELGSQIEEATYQELR

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	36.76 RPM
SRP051959_heart	0.04 RPM	34.83 RPM
SRP051959_kidney	0.31 RPM	45.57 RPM
SRP051959_liver	0.24 RPM	37.43 RPM
SRP051959_lung	0.08 RPM	45.84 RPM
SRP051959_lymph_node	0.14 RPM	64.22 RPM
SRP051959_skeletal_muscle	0.04 RPM	30.35 RPM
SRP051959_spleen	0.13 RPM	51.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2095 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2095 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2095 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095 ,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,