RetrogeneDB ID: retro_mdom_964

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:42065170..42065866(+)
• Located in intron of: ENSMODG00000001045

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCAMP1
• Ensembl ID: ENSMODG00000019731
• Aliases: None
• Description: secretory carrier membrane protein 1 [Source:HGNC Symbol;Acc:10563]

Sequence

>retro_mdom_964
AGCAACCCGTTCACAGACTCGGATTTCAACAACCCTTTCAAGGATCCATCAGTTACATAGGTGACTGGAAATATGCCACC
AGGGCTTAATGAATATAATCCATTTTCTGATTCTAGAACCGCACCACCAGGAAATGTGAAAATGCCTAATGTACCTAGTA
CACAACCAGCGATAATGAAGCCAAAAGAAGAAGCCCCAACTTATACACAAATTGCAAAGGCACATGTTTTGGCTCAAGCT
GACCTGATTAAACATCAAGAGCTAGAAAGAAAAGCAGTAGAGTGAGATCACTGAGAAAGAGAAATGCAGAGCCTCAATCA
GCATGGTGGCAGAAAAAATAATTGGCCATCTCTTTCTGGGAATTTTCCAGTGGGACCTTGTTTCTATCAGGATTTTTCTG
TAGACAACCTTGTAGAATTTCAGAAGACAGTAAAGATTATGTACTACTTGTGAATGTTCCATGCTGTAATACTGTTCCTA
AATATCTTTGGATGCTTGATGTGGTTTTGTGTTGAGCCTGGACGAGGGGTTGATTTTGGATTGAGAATCCTCTGGTTCAT
GCCTTTCATGCCTTGTTCATTTGTCTGTTGATACAGACCACTTTATGGAGCTTTCAGGAATGATAGTTCCTTCAGATTAT
TTGTGTATATTTGTCAGTTTGCTGTACATGTGCTTCAGGCTGCAGGGCAATTGTGG

Alignment

ORF - retro_mdom_964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 70.21 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDTFVSPDLCNPFEDPSVTQVTRNMPPGLDEYNPFSDSRTAPPGNVKMPNVPSTQPAIMKPTEEAPTYTQ
          S..F...D..NPF.DPSVT.VT.NMPPGL.EYNPFSDSRTAPPGNVKMPNVPSTQPAIMKP.EEAPTYTQ
Retrocopy SNPFTDSDFNNPFKDPSVT*VTGNMPPGLNEYNPFSDSRTAPPGNVKMPNVPSTQPAIMKPKEEAPTYTQ

Parental  IAKEHALAQAELLKRQEELERKAAELDRREREMQSLNQHGGRKNNWPPLPGNFPVGPCFYQDFSVDIPVE
          IAK.H.LAQA.L.K.QE.LERKA.E.D..EREMQSLNQHGGRKNNWP.L.GNFPVGPCFYQDFSVD..VE
Retrocopy IAKAHVLAQADLIKHQE-LERKAVE*DH*EREMQSLNQHGGRKNNWPSLSGNFPVGPCFYQDFSVDNLVE

Parental  FQKTVKIMYYLWMFHAVTLFLNIFGCLAWFCVEPGRGVDFGLSILWFMLFTPCSFVCWYRPLYGAFRSDS
          FQKTVKIMYYL.MFHAV.LFLNIFGCL.WFCVEPGRGVDFGL.ILWFM.F.PCSFVC.YRPLYGAFR.DS
Retrocopy FQKTVKIMYYL*MFHAVILFLNIFGCLMWFCVEPGRGVDFGLRILWFMPFMPCSFVC*YRPLYGAFRNDS

Parental  SFRFFVFFFVYICQFAVHVLQAAGFQSW
          SFR.FV.....ICQFAVHVLQAAG.Q.W
Retrocopy SFRLFVY----ICQFAVHVLQAAG-QLW

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_964 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_964 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,