RetrogeneDB ID: retro_mdom_1428

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:10950651..10951482(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OLA1
• Ensembl ID: ENSMODG00000009296
• Aliases: None
• Description: Obg-like ATPase 1 [Source:HGNC Symbol;Acc:28833]

Sequence

>retro_mdom_1428
CTCTTTCATTTAAAGCAATCATGTGAAGATGATGATATCACTCACATTGAAGGAAGTGTAGATCCTGTTCGAGACATTGA
AATAATACCTGAAGAGCTTCTACTTAAAGATGAGGAAATGATCATGCCCATACTAGATAAACTAGAAAAGGTGGCTATGA
GAGGAGGAGACAAGAAATTAAAACCTGAATATGACATAATGTGCAAAATTAAAACTTGGGTTATAGATGAAAAGAAACCT
GTACACTTCTATCACGACTGCAATGACAAAGAGATTGAAATGTTGAATAAACACTTGCTTTTGACTTCAAAACCAATGAT
CTACTCATTTATCCTTTCAGAAAAGGACTACATTAGAAAGAAAAAGAAATGGTTGATAAAAATTAAAGAGTAGGTAGACA
AGCATGACCCAGGGGCCTTGGCCATTCCTTTTAGTGGGGCCTTGGAACTCAAGTTGCAAGAAATGAGTGCTGAGGAGAAA
CAGAAGTATCTGGAAGAGAACATGGCACAAAGTGCTTTACCAAAGATCATCAAGGCTGGCTATGCAGCACTCCAACTAGA
ATACTTTTTCACTGCAGACCCAGATGAAGAACGTGCATAACCCATCAGCAAAGTGACGAAGGCTCCTCAGGCAGCAGGAA
AGATTCACACCAGTTTTGAAAAGGGATTCATTATGGCTTAAGTAATGAAATATGAAGATTTTAAAGAGGAAGGTTCAGAA
AATGCTGTCAAGGCTGCTGGGAAATACAGACAACAAGGTAGAAATTACAAAATTGAAGATGGAAATATTATCTTCTTTAA
ATTTAATATACCTCAGCAACCTAAGAAGAAA

Alignment

ORF - retro_mdom_1428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.95 %
• Parental protein coverage: 69.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IFHLMRSFEDDDITHIEGSVDPVRDIEIIHEELRLKDEEMIMPIIDKLEKVAVRGGDKKLKPEYDIMCKI
          .FHL..S.EDDDITHIEGSVDPVRDIEII.EEL.LKDEEMIMPI.DKLEKVA.RGGDKKLKPEYDIMCKI
Retrocopy LFHLKQSCEDDDITHIEGSVDPVRDIEIIPEELLLKDEEMIMPILDKLEKVAMRGGDKKLKPEYDIMCKI

Parental  KTWVIDEKKPVRFYHDWNDKEIEVLNKHLFLTSKPMIYLVNLSEKDYIRKKNKWINAIKRYPCKIALSAP
          KTWVIDEKKPV.FYHD.NDKEIE.LNKHL.LTSKPMIY...LSEKDYIRKK.KW...IK....K....A.
Retrocopy KTWVIDEKKPVHFYHDCNDKEIEMLNKHLLLTSKPMIYSFILSEKDYIRKKKKWLIKIKE*VDKHDPGAL

Parental  KLEFVGQAGHQLQEMSAEEKQKYLEENMTQSALPKIIKAGYAALQLEYFFTAGPDEVRAWTIRKGTKAPQ
          ...F.G.....LQEMSAEEKQKYLEENM.QSALPKIIKAGYAALQLEYFFTA.PDE.RA..I.K.TKAPQ
Retrocopy AIPFSGALELKLQEMSAEEKQKYLEENMAQSALPKIIKAGYAALQLEYFFTADPDEERA*PISKVTKAPQ

Parental  AAGKIHTDFEKGFIMAEVMKYEDFKEEGSENAVKAAGKYRQQGRNYIVEDGDIIFFKFNTPQQPKKK
          AAGKIHT.FEKGFIMA.VMKYEDFKEEGSENAVKAAGKYRQQGRNY..EDG.IIFFKFN.PQQPKKK
Retrocopy AAGKIHTSFEKGFIMA*VMKYEDFKEEGSENAVKAAGKYRQQGRNYKIEDGNIIFFKFNIPQQPKKK

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_1428 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1428 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 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006970	1 retrocopy	retro_btau_1737,
Choloepus hoffmanni	ENSCHOG00000005044	1 retrocopy	retro_chof_1295,
Callithrix jacchus	ENSCJAG00000007877	1 retrocopy	retro_cjac_2875,
Dipodomys ordii	ENSDORG00000008681	1 retrocopy	retro_dord_556,
Homo sapiens	ENSG00000138430	1 retrocopy	retro_hsap_2593,
Gorilla gorilla	ENSGGOG00000022215	1 retrocopy	retro_ggor_1623,
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428 ,
Nomascus leucogenys	ENSNLEG00000005817	1 retrocopy	retro_nleu_1526,
Otolemur garnettii	ENSOGAG00000016557	1 retrocopy	retro_ogar_1697,
Pongo abelii	ENSPPYG00000012943	2 retrocopies	retro_pabe_1912, retro_pabe_928,
Pan troglodytes	ENSPTRG00000012650	1 retrocopy	retro_ptro_1517,
Rattus norvegicus	ENSRNOG00000019047	1 retrocopy	retro_rnor_2219,
Sorex araneus	ENSSARG00000010743	1 retrocopy	retro_sara_545,
Tupaia belangeri	ENSTBEG00000007574	8 retrocopies	retro_tbel_1749, retro_tbel_2506, retro_tbel_3217, retro_tbel_3581, retro_tbel_418, retro_tbel_4356, retro_tbel_4475, retro_tbel_88,
Tarsius syrichta	ENSTSYG00000005517	2 retrocopies	retro_tsyr_1845, retro_tsyr_394,
Vicugna pacos	ENSVPAG00000009660	2 retrocopies	retro_vpac_52, retro_vpac_613,