RetrogeneDB ID: retro_mdom_764

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:389318624..389319304(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZMYND19
• Ensembl ID: ENSMODG00000017172
• Aliases: None
• Description: zinc finger, MYND-type containing 19 [Source:HGNC Symbol;Acc:21146]

Sequence

>retro_mdom_764
ATGACCGATTTCAATCTGGGCATCATGCGGCTCAGTCGAGCGGCTGGGAAGACAAAGTACACGCTGATAGATGAACAAGA
CATCCCACTGGTGGAGAGTTACTCTTTTGAGGCATGAATGGAAGTAGATGCTGATGGAAATGGTGCTAAAATATTTGCTT
ATGCTTTTGATAAAAACCGAGGAAGGGGATCTGGACGTTTATTTCATGAGTTGTTGTGGGAACGACACAGGGGAGGAATT
GCTCCAGGATTTCAAGTGGTACATCTTAATGCAGTAACTGTGGACAATCGATTAGACAACCTGCATTTAGTACCATGGGT
CTGGAGACCGAAAGCAGAAGAAATCTCTAGTAAGCAAAGGGAGCAGAGCCTGTACTGGCTTGCAATTCAGCAGCTTCCCA
CTGATCCTATTGAAGAACAGTTCCCTGTCCTGAATGTTACTCGCTATTATAATGCTAATGGAGATGTGGTAGAAGAAGAG
GAGAATTCCTGCACATACTATGAATGTCATTATCCCCCATGCACAATGTTTGAAAAGCAGTTACTTGAATTCAACATCTG
TGGCGGTGTTAGGTGGCCAGGTACTGTGGTTCCCAGTGCCAGCAAAAGAATTGCCCTGCTCACAAGAAACATTGTCGGGA
GAAGAAACGAACCTTCCAGCAAGAGCTTGAACCAGAGCGA

Alignment

ORF - retro_mdom_764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTDFKLGIVRLGRVAGKTKYTLIDEQDIPLVESYSFEARMEVDADGNGAKIFAYAFDKNRGRGSGRLLHE
          MTDF.LGI.RL.R.AGKTKYTLIDEQDIPLVESYSFEA.MEVDADGNGAKIFAYAFDKNRGRGSGRL.HE
Retrocopy MTDFNLGIMRLSRAAGKTKYTLIDEQDIPLVESYSFEA*MEVDADGNGAKIFAYAFDKNRGRGSGRLFHE

Parental  LLWERHRGGIAPGFQVVHLNAVTVDNRLDNLQLVPWGWRPKAEEISSKQREQSLYWLAIQQLPTDPIEEQ
          LLWERHRGGIAPGFQVVHLNAVTVDNRLDNL.LVPW.WRPKAEEISSKQREQSLYWLAIQQLPTDPIEEQ
Retrocopy LLWERHRGGIAPGFQVVHLNAVTVDNRLDNLHLVPWVWRPKAEEISSKQREQSLYWLAIQQLPTDPIEEQ

Parental  FPVLNVTRYYNANGDVVEEEENSCTYYECHYPPCTMIEKQLREFNICG-RCQVARYCGSQCQQKDWPAHK
          FPVLNVTRYYNANGDVVEEEENSCTYYECHYPPCTM.EKQL.EFNICG.RC.VARYCGSQCQQK..PAHK
Retrocopy FPVLNVTRYYNANGDVVEEEENSCTYYECHYPPCTMFEKQLLEFNICG<RC*VARYCGSQCQQKNCPAHK

Parental  KHCREKKRTFQQELEPER
          KHCREKKRTFQQELEPER
Retrocopy KHCREKKRTFQQELEPER

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	88.09 RPM
SRP007412_cerebellum	0.00 RPM	92.71 RPM
SRP007412_heart	0.00 RPM	44.26 RPM
SRP007412_kidney	0.00 RPM	38.19 RPM
SRP007412_liver	0.00 RPM	50.35 RPM
SRP007412_testis	0.00 RPM	484.99 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_764 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_764 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006644	2 retrocopies	retro_dnov_1389, retro_dnov_1468,
Dipodomys ordii	ENSDORG00000008360	1 retrocopy	retro_dord_390,
Equus caballus	ENSECAG00000012412	1 retrocopy	retro_ecab_903,
Echinops telfairi	ENSETEG00000005023	1 retrocopy	retro_etel_1068,
Homo sapiens	ENSG00000165724	1 retrocopy	retro_hsap_1367,
Gorilla gorilla	ENSGGOG00000006875	1 retrocopy	retro_ggor_1065,
Macropus eugenii	ENSMEUG00000011727	1 retrocopy	retro_meug_2010,
Macaca mulatta	ENSMMUG00000019610	1 retrocopy	retro_mmul_2195,
Monodelphis domestica	ENSMODG00000017172	1 retrocopy	retro_mdom_764 ,
Mus musculus	ENSMUSG00000026974	3 retrocopies	retro_mmus_1433, retro_mmus_2466, retro_mmus_942,
Nomascus leucogenys	ENSNLEG00000009236	1 retrocopy	retro_nleu_1071,
Tursiops truncatus	ENSTTRG00000010812	1 retrocopy	retro_ttru_900,