RetrogeneDB ID: retro_mdom_720

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:227231084..227231558(+)
• Located in intron of: ENSMODG00000004147

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSMODG00000018634
• Aliases: None
• Description: pleckstrin homology domain containing, family B (evectins) member 2 [Source:HGNC Symbol;Acc:19236]

Sequence

>retro_mdom_720
GATTTTCATCCTCCTGAGGGCAAACCAAAAGACAGAATAATGCAAATTGTTTGCTGAGATGGAAAAACTATCAATCTTTG
TGCAGAAAGTGCTGATGATTGCTTGGCCTGGCAATTTGTTCTCTAGGATGCCAGGACAAATACAGGCTATGTTGCCTCAG
AAGTCATGAAGGATGAGACTGCAGTTGCTTCATCTCCTCCTCCTTACACAGCATATGCCACACCATCCCCTGAGGTATTT
GGCTACAGTCACTATAATGGCACATACCCTCCAGGAACTCAAGTCATCTATGCTGCTAATGGACAGGCTTATGCAGTACC
ATATCAGTATCCATATCCAGGACCTTATGGACAGCAGCCTGCCAATCATGTCATCATTAGGGAGTGTTACCGGGACAACG
ATGGAGACCTGGCTCTGGGCATGCTGGCTGGAGCAGCCACTGGCGTGGCCTTGGGATCTTTGTTCTGGGTCTTC

Alignment

ORF - retro_mdom_720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.94 %
• Parental protein coverage: 71.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFHPPEGKPKDRILQIVCRDGKNINLCAESADDCLAWQFALQDARTNTGYVASEVMYDETAVASSPPPYT
          DFHPPEGKPKDRI.QIVC.DGK.INLCAESADDCLAWQF.L.DARTNTGYVASEVM.DETAVASSPPPYT
Retrocopy DFHPPEGKPKDRIMQIVC*DGKTINLCAESADDCLAWQFVL*DARTNTGYVASEVMKDETAVASSPPPYT

Parental  AYATPSPEVFGYSHYNGTYPPGTQVIYAANGQAYAVPYQYPYPGPYGQQPANHVIIRERYRDNDGDLALG
          AYATPSPEVFGYSHYNGTYPPGTQVIYAANGQAYAVPYQYPYPGPYGQQPANHVIIRE.YRDNDGDLALG
Retrocopy AYATPSPEVFGYSHYNGTYPPGTQVIYAANGQAYAVPYQYPYPGPYGQQPANHVIIRECYRDNDGDLALG

Parental  MLAGAATGMALGSLFWVF
          MLAGAATG.ALGSLFWVF
Retrocopy MLAGAATGVALGSLFWVF

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_720 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_720 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720 ,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471, retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56,