RetrogeneDB ID: retro_mmul_396

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:99447291..99447893(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCAMP1
• Ensembl ID: ENSMMUG00000016398
• Aliases: None
• Description: secretory carrier membrane protein 1 [Source:HGNC Symbol;Acc:10563]

Sequence

>retro_mmul_396
TTGGCCCAAGCTGAACTTCTTAAACACCAAGAAGAAGTAGAAAGAAAAGATGCATAATTCAATCATCGGGAATGAGAAAT
GCAAAACCTCACTCAACATGGTAGAAAAAATAATTGGCCACTTCTTCTCAGCAATTTTCCTATAGAACCTTGTTTCTATC
AGGATTTTTCTGTGACATTCCTATAGAATTCCAAAAGACAGTAAAGCTTATATACTACTTCTGGATGTTCCATGCTGTAA
CACTGTTTCCAAATATCTTCAGATGCTTGTCTTGGTTTTGTGTTGATTTCATAAGAGTGGTTGATTTTGGATTGAGTATC
CCGTGGTTCTTGCTTTTTACTCCTTGTTCATTTGTCTGTTGGTACAGACCACTTTACGGAGCTTTCAGGAGTGATAGTTC
ATTCAGATTCTTTGTATTCTTCTTCGTCTATATTTGTTAGTTTGCTGTACATGCATTCCAGGCTGTAGGATTTCATAACT
GGGGCAATTGTGGTTGAATTTCAACCCTTACTGGTCTCAACCAAACTATTCCTGTTGGAATCAGGATGATAATCATAGCA
GCACTTTTTGCAGCATCAGCAGCCATCTCACTAGTTATGTTT

Alignment

ORF - retro_mmul_396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.17 %
• Parental protein coverage: 62.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAQAELLKRQEELERKAAELDRREREMQNLSQHGRKNNWPPLPSNFPVGPCFYQDFSV-DIPVEFQKTVK
          LAQAELLK.QEE.ERK.A....RE.EMQNL.QHGRKNNWP.L.SNFP..PCFYQDFSV.DIP.EFQKTVK
Retrocopy LAQAELLKHQEEVERKDA*FNHRE*EMQNLTQHGRKNNWPLLLSNFPIEPCFYQDFSV<DIPIEFQKTVK

Parental  LMYYLWMFHAVTLFLNIFGCLAWFCVDSARAVDFGLSILWFLLFTPCSFVCWYRPLYGAFRSDSSFRFFV
          L.YY.WMFHAVTLF.NIF.CL.WFCVD..R.VDFGLSI.WFLLFTPCSFVCWYRPLYGAFRSDSSFRFFV
Retrocopy LIYYFWMFHAVTLFPNIFRCLSWFCVDFIRVVDFGLSIPWFLLFTPCSFVCWYRPLYGAFRSDSSFRFFV

Parental  FFFVYICQFAVHVLQAAGFHNWGNCGWISSLTGLNQNIPVGIMMIIIAALFTASAVISLVMF
          FFFVYIC.FAVH..QA.GFHNWGNCG.IS.LTGLNQ.IPVGI.MIIIAALF.ASA.ISLVMF
Retrocopy FFFVYIC*FAVHAFQAVGFHNWGNCG*ISTLTGLNQTIPVGIRMIIIAALFAASAAISLVMF

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
SRP007412_brain	0.00 RPM	46.28 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	31.26 RPM
SRP007412_cerebellum	0.00 RPM	29.70 RPM
SRP007412_heart	0.00 RPM	4.65 RPM
SRP007412_kidney	0.00 RPM	9.04 RPM
SRP007412_liver	0.00 RPM	1.82 RPM
SRP007412_testis	0.00 RPM	16.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_396 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_396 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_189
Gorilla gorilla	retro_ggor_269

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032395	1 retrocopy	retro_cfam_227,
Cavia porcellus	ENSCPOG00000008868	1 retrocopy	retro_cpor_174,
Homo sapiens	ENSG00000085365	1 retrocopy	retro_hsap_189,
Gorilla gorilla	ENSGGOG00000015191	1 retrocopy	retro_ggor_269,
Macaca mulatta	ENSMMUG00000016398	1 retrocopy	retro_mmul_396 ,
Monodelphis domestica	ENSMODG00000019731	1 retrocopy	retro_mdom_964,
Nomascus leucogenys	ENSNLEG00000012775	1 retrocopy	retro_nleu_1000,
Tarsius syrichta	ENSTSYG00000014113	1 retrocopy	retro_tsyr_1676,