RetrogeneDB ID: retro_cjac_2001

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:1025875..1026762(-)
• Located in intron of: ENSCJAG00000018324

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSCJAG00000018176
• Aliases: None
• Description: None

Sequence

>retro_cjac_2001
TACTCTAGGGATTATTATAGATGTGATGACAGAGGTCCCTGCCAAAGACCCAAATTGGATCTGAAGCCTCAGAGTACTCC
TAAGGAAGATGATTCCTCAGCTAGTACCTCCCTGTCGAGTCAAGCTGCTTCTATCTTTGGAGGGGCAAAGTCCATTCACA
CAGCTGCTAGAGAAAGAGAAGTAAAAGAACGCCTACAGAAGGAACAAGAGAAGCTGCAGTGTCAGTTGGATGAGCCAAAA
CTAGAACGATCGTCTCGGGAGAGACATCCAAGCAGGTGAAGTAAAAAAAACTCAGGAACTGGAACAGTTGAGGACAGGAA
GTGAGTCTTCACAGACTGGGACCTCCACCACATCCCACAGAAATGCACGAAGGAGAGAGTGAGAAGTCTACAGAAAATGA
AACACTCAATAAGGAGGAAGATTGTCACTCTGCAACGTCTAAGCCTCTTAAACCTGATCAGTCTCTAAAGGAAATGTCAG
CCTCTCCACCAAAGGAGAATGCTTCTGTGAAACAAAGTTCTAACTCTCCTGCTCCATCTCAAAGCTCAAACACAGGGCAG
CAAACCCCTACAAATAGTGGGGGGAAAGTAGTTCCAGCTTAACCAACTGAGGAAAGACCAGCAAGGAAAGATGAAAATAA
AGTAGATGGGATAAATTTCCCAAAAGGCCAAAGTAGGAACTCTAGCTGTGGTCCAGGAGACAGAGGGAACGAAGACCACT
GGAAGGAGTCAGATAGGAAAGACAGCAAAAAGGATCAAGACTCCAGATCTGCACCTGAGCCAAAGAAACCTGAGGAAAAT
CCAGCCTCCAAGTTCAGTTCTGCAAGCAAGTATGCTGCTCTCTTCATTGATGGTGAAGATGAAAACAAGGTTGAAGATTA
CGCTAAA

Alignment

ORF - retro_cjac_2001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.52 %
• Parental protein coverage: 80.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YSWDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTSQSSRAASIFGGAKPVDTAAREREVEERLQKEQE
          YS.D.YR.DDRGP.QRPKL.LKP.STPKEDDSSASTS.SS.AASIFGGAK...TAAREREV.ERLQKEQE
Retrocopy YSRDYYRCDDRGPCQRPKLDLKPQSTPKEDDSSASTSLSSQAASIFGGAKSIHTAAREREVKERLQKEQE

Parental  KLQRQLDEPKLERRPRERHPSWRSEE-TQERERSRTGSESSQTGTSATSGRNARRR-ESEKSLENETLSK
          KLQ.QLDEPKLER..RERHPS..S...TQE.E..RTGSESSQTGTS.TS.RNA.RR.ESEKS.ENETL.K
Retrocopy KLQCQLDEPKLERSSRERHPSR*SKK>TQELEQLRTGSESSQTGTSTTSHRNA-RR>ESEKSTENETLNK

Parental  EEDCHSPTSKPPKPDQPLKVMPAPPPKENAWVKRSSNPPARSQSSDTEQQSPTSGGGKVAPAQPSEEGPA
          EEDCHS.TSKP.KPDQ.LK.M.A.PPKENA.VK.SSN.PA.SQSS.T.QQ.PT..GGKV.PA.P.EE.PA
Retrocopy EEDCHSATSKPLKPDQSLKEMSASPPKENASVKQSSNSPAPSQSSNTGQQTPTNSGGKVVPA*PTEERPA

Parental  RKDENKIDGMNVPKGQTGNSSRGPGDGVNKDHWKESDRKDGKKDQDSRSAPEPKKPEENPASMFSSASKY
          RKDENK.DG.N.PKGQ..NSS.GPGD..N.DHWKESDRKD.KKDQDSRSAPEPKKPEENPAS.FSSASKY
Retrocopy RKDENKVDGINFPKGQSRNSSCGPGDRGNEDHWKESDRKDSKKDQDSRSAPEPKKPEENPASKFSSASKY

Parental  AALSVDGEDENEGEDYAE
          AAL..DGEDEN..EDYA.
Retrocopy AALFIDGEDENKVEDYAK

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	171.18 RPM
SRP051959_heart	0.33 RPM	187.14 RPM
SRP051959_kidney	0.22 RPM	193.02 RPM
SRP051959_liver	0.13 RPM	184.59 RPM
SRP051959_lung	0.16 RPM	199.21 RPM
SRP051959_lymph_node	0.18 RPM	224.10 RPM
SRP051959_skeletal_muscle	0.33 RPM	200.47 RPM
SRP051959_spleen	0.29 RPM	231.93 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2001 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2001 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001 ,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,