RetrogeneDB ID: retro_cjac_4025

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL289525.1:4848..5290(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSCJAG00000002354
• Aliases: None
• Description: spermidine synthase [Source:HGNC Symbol;Acc:11296]

Sequence

>retro_cjac_4025
GAGCCCAGCCCCAAGGGCCCAGCTGCCTCCCACCCGCTGCCATCCACGAGGACTGGTTCCAAGGGAACTGCAGCCTGTGG
CTCAGCCAGGCCTTGTTGCTGCAGCTGCAGCAGCTGCTCCAAACTCAGTGCACATGCTCCCAGGAAATCCTCACCTGCAG
CCAGACTTATGGCCACGTGCTGGTGTCATGCGTGTCATCCAATGCACAGAGGGGGATGAGTTCTCCCCCTCGGAGCTGAT
CGTCCACCTGCCTCTCTGCAGCTTCCCCCTCCCGCCCCCAACAGGTGCTGACCATCCAGGTCCTGTGCGAGGTGGTGAAA
CACATCGCTCCGCGGAGTCCGTGGTCAAGTGTGAGATCGTCGAAGATGTCCTCCAAGTCCCCAAAAAGTTCCTGCTGGGC
ATGGCTATTGGCTAGTCTAGCTTGAAGCTGACCATGTGGGTG

Alignment

ORF - retro_cjac_4025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 50.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESGPDGPAASGP-AAIREGWFR-ETQLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLV-LDGVI
          E..P.GPAAS.P.AAI.E.WF.....LW..QAL.LQ..QLL.......Q.IL...S.TYG.VLV....VI
Retrocopy EPSPKGPAASHP<AAIHEDWFQGNCSLWLSQALLLQLQQLLQTQCTCSQEILTC-SQTYGHVLV<VMRVI

Parental  QCTERDEFSYQEMIANLPLCSHPNPQKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPG
          QCTE.DEFS..E.I..LPLCS.P.P......G....G..R....H.S.ESVV.CEI.EDV.QV.KKFL.G
Retrocopy QCTEGDEFSPSELIVHLPLCSFPLPPPT---GADHPGPVRGGETHRSAESVVKCEIVEDVLQVPKKFLLG

Parental  MAVGYSSSKLTLHV
          MA.G.SS.KLT..V
Retrocopy MAIG*SSLKLTMWV

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	0.00 RPM	4.06 RPM
SRP051959_heart	0.00 RPM	3.82 RPM
SRP051959_kidney	0.00 RPM	3.59 RPM
SRP051959_liver	0.00 RPM	6.28 RPM
SRP051959_lung	0.00 RPM	3.35 RPM
SRP051959_lymph_node	0.00 RPM	4.68 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.22 RPM
SRP051959_spleen	0.00 RPM	4.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4025 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4025 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4025 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025 ,
Dasypus novemcinctus	ENSDNOG00000013348	1 retrocopy	retro_dnov_338,
Homo sapiens	ENSG00000116649	2 retrocopies	retro_hsap_1426, retro_hsap_2313,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Loxodonta africana	ENSLAFG00000028297	2 retrocopies	retro_lafr_1175, retro_lafr_894,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259,
Mus musculus	ENSMUSG00000006442	1 retrocopy	retro_mmus_3271,
Nomascus leucogenys	ENSNLEG00000009532	3 retrocopies	retro_nleu_1842, retro_nleu_2082, retro_nleu_2778,
Ochotona princeps	ENSOPRG00000012079	1 retrocopy	retro_opri_1119,
Pongo abelii	ENSPPYG00000001892	3 retrocopies	retro_pabe_1181, retro_pabe_1828, retro_pabe_2044,
Pan troglodytes	ENSPTRG00000000138	3 retrocopies	retro_ptro_1403, retro_ptro_1688, retro_ptro_975,