RetrogeneDB ID: retro_cjac_3735

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01197699.1:25..748(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF1AL7
• Ensembl ID: ENSCJAG00000010051
• Aliases: None
• Description: None

Sequence

>retro_cjac_3735
AAAGAAAGGACTCATATCAACACCGTCGTCATTGTCCATGTAGATCTGGGAATTCCACCATTCCTGGCCATCTGATCTAC
ACAGGTGGTGGCCTGGACAAACAAATCACTGAAAATGTGAGGAGGAGGCTGCTGAGTTGGGAATGGGCTCTTCAGTGTGC
CTGTGTCTTGGATAAACTGAAAGCTGAGTGTGAATGTGATACTACCTTGACGTCTTCCTTTAGAAATCTGAGACCAGCAA
GTACCAGTGACTATCGTTGATGCTTCAGGCCATAGAGACTATATCAGCAACATGAATACAGGCTCATTTCAGACGGGCTG
TGCTATTCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTATCTCCAAGAATGGGCAGACCCATGAGCCTGACC
TTCTGGCTCACACGCTGGGTATGAAACAACTAATTGTTGTGTCAACAATATGGATTCCATGGAGCCACTCTCCAGCCAGA
AGAGACATGAAGAAACTGTGAAGGAAGTCAGCACCTACACTGAGAAAACTGCGTACAACCCTGGCACGTAGCATTTGTGG
TAGCTTCTGTTTGAAATAGCAACAGCATGCCGGAGCCAGGAGCTCATAGGCCTTGGTTCCAGGATGGAAAGTCACCCTTA
GAGATGGCAATGCCAGGGAAAACATGCTGCTGGGAGCTCTGGACATCTTCCTACCACCAACTGGTCAGACTGACAAGCCC
GTC

Alignment

ORF - retro_cjac_3735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.43 %
• Parental protein coverage: 52.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  KEKTHINIVVIGHVD-SGKSTTTGHLIYKCGGIDKRTIE-KFEKEAAEM-GKGSFKY-AWVLDKLKAERE
          KE.THIN.VVI.HVD.SG.ST..GHLIY..GG.DK...E.K.E.EAAE..G.G.F...A.VLDKLKAE.E
Retrocopy KERTHINTVVIVHVD<SGNSTIPGHLIYTGGGLDKQITE<KCEEEAAEL<GNGLFSV<ACVLDKLKAECE

Parental  RGITI-DISLWKFETSKYY-VTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREH
          ...T..D..L.K.ETSKY..VTI.DA.GHRD.I.NM.TG..Q..CA.LIVAAGVGEFEAGISKNGQT.E.
Retrocopy CDTTL<DVFL*KSETSKYQ<VTIVDASGHRDYISNMNTGSFQTGCAILIVAAGVGEFEAGISKNGQTHEP

Parental  ALLAYTLGVKQLIV-GVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDT-VAFVPISGWNGDNMLEP
          .LLA.TLG.KQLIV..VN.MDS.EP..SQKR.EE.VKEVSTY..K..YNP.T.VAFV..S..N...M.EP
Retrocopy DLLAHTLGMKQLIV<CVNNMDSMEPLSSQKRHEETVKEVSTYTEKTAYNPGT<VAFVVASV*NSNSMPEP

Parental  SANMPWFK-GWKVTRKDGNASGTTLLEALDCILPPTRPTDKPL
          .A..PWF..GWKVT..DGNA....LL.ALD..LPPT..TDKP.
Retrocopy GAHRPWFQ<GWKVTLRDGNARENMLLGALDIFLPPTGQTDKPV

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	1829.24 RPM
SRP051959_heart	0.40 RPM	1562.48 RPM
SRP051959_kidney	0.07 RPM	2044.86 RPM
SRP051959_liver	0.09 RPM	2887.01 RPM
SRP051959_lung	0.03 RPM	2118.54 RPM
SRP051959_lymph_node	0.00 RPM	2452.64 RPM
SRP051959_skeletal_muscle	0.02 RPM	749.17 RPM
SRP051959_spleen	0.08 RPM	2786.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3735 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3735 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Callithrix jacchus	ENSCJAG00000010051	6 retrocopies	retro_cjac_1431, retro_cjac_3075, retro_cjac_34, retro_cjac_3735 , retro_cjac_733, retro_cjac_97,
Cavia porcellus	ENSCPOG00000004067	15 retrocopies	retro_cpor_1150, retro_cpor_1162, retro_cpor_1191, retro_cpor_1256, retro_cpor_1393, retro_cpor_1492, retro_cpor_1499, retro_cpor_348, retro_cpor_381, retro_cpor_387, retro_cpor_413, retro_cpor_709, retro_cpor_891, retro_cpor_918, retro_cpor_959,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Macaca mulatta	ENSMMUG00000004852	15 retrocopies	retro_mmul_1375, retro_mmul_1407, retro_mmul_1518, retro_mmul_1525, retro_mmul_1690, retro_mmul_1707, retro_mmul_1721, retro_mmul_1739, retro_mmul_1743, retro_mmul_1906, retro_mmul_2196, retro_mmul_2250, retro_mmul_323, retro_mmul_6, retro_mmul_848,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Pan troglodytes	ENSPTRG00000018347	1 retrocopy	retro_ptro_71,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,