RetrogeneDB ID: retro_mdom_1215

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:502081610..502082111(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX24
• Ensembl ID: ENSMODG00000013427
• Aliases: None
• Description: sorting nexin 24 [Source:HGNC Symbol;Acc:21533]

Sequence

>retro_mdom_1215
GTCTACATTCCATCTTTTTGTTATGAAAAGAGTGATCTGGAGAGAGACTACATGGTCTTTTAAGAAAGAAGTGCTAATGA
GTGGACAGAAGCATTTTGTAGAAAAAAAGTATAGCAAATTTCAAGCTCTGCATAAAAAGTTCAAGAAATGTATAAAAACT
CCAGAAATTCCTTCCAAACAGATTAGAAACTGGGTCCCAAAGGTCCTGGAGCAGCGACAACAAAGTTTAGGAGTCTATTT
ACAGTTATCGTTTTGGAAAAAGAGCTTCTAAAATTATTTCTTGATTTTCTAAATGTATGACATTTACCTTCTCTACCAAA
GACAGAAAGTTGTGGCTCATTTGAGGAAACAAAATCTGAAGAATACAGCAAACTGTCCCACCTACCAGTGGTGCTGTTCC
TAAGGGATCCACATGTCTTGCCTACAGCCAACGATGATTTTCCAGATGTAGTTACTGAAGGAGTTCTCCATGAGATAGTT
TACCCTCCTCTACAGCCCAGG

Alignment

ORF - retro_mdom_1215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.82 %
• Parental protein coverage: 98.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VYIPSFRYEESDLERGYTVF-KIEVLMSGRKHFVEKRYSEFHALHKKLKKCIKTPEIPSKHVRNWVPKVL
          VYIPSF.YE.SDLER.Y.VF.K.EVLMSG.KHFVEK.YS.F.ALHKK.KKCIKTPEIPSK..RNWVPKVL
Retrocopy VYIPSFCYEKSDLERDYMVF>KKEVLMSGQKHFVEKKYSKFQALHKKFKKCIKTPEIPSKQIRNWVPKVL

Parental  EQRRQGLEAYLQ-AVILENEELPKFFLDFLNVRHLPSLPKTESCGSFEETESEESSKLSHQPVLLFLRDP
          EQR.Q.L..YLQ....LE..EL.K.FLDFLNV.HLPSLPKTESCGSFEET.SEE.SKLSH.PV.LFLRDP
Retrocopy EQRQQSLGVYLQ<VIVLE-KELLKLFLDFLNV*HLPSLPKTESCGSFEETKSEEYSKLSHLPVVLFLRDP

Parental  YVLPTANDDFPNVVIEGVLHGIFYPHLQPR
          .VLPTANDDFP.VV.EGVLH.I.YP.LQPR
Retrocopy HVLPTANDDFPDVVTEGVLHEIVYPPLQPR

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_1215 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1215 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031069	1 retrocopy	retro_btau_640,
Choloepus hoffmanni	ENSCHOG00000006859	2 retrocopies	retro_chof_1841, retro_chof_544,
Dasypus novemcinctus	ENSDNOG00000019810	1 retrocopy	retro_dnov_261,
Echinops telfairi	ENSETEG00000010310	1 retrocopy	retro_etel_923,
Microcebus murinus	ENSMICG00000001708	1 retrocopy	retro_mmur_1043,
Myotis lucifugus	ENSMLUG00000009392	2 retrocopies	retro_mluc_1022, retro_mluc_2330,
Monodelphis domestica	ENSMODG00000013427	1 retrocopy	retro_mdom_1215 ,
Otolemur garnettii	ENSOGAG00000005170	2 retrocopies	retro_ogar_2940, retro_ogar_975,
Sorex araneus	ENSSARG00000009785	1 retrocopy	retro_sara_99,
Sarcophilus harrisii	ENSSHAG00000011329	1 retrocopy	retro_shar_488,
Tarsius syrichta	ENSTSYG00000014395	2 retrocopies	retro_tsyr_1563, retro_tsyr_1691,