RetrogeneDB ID: retro_mdom_1602

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:126746681..126747210(+)
• Located in intron of: ENSMODG00000008224

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP30BP
• Ensembl ID: ENSMODG00000007562
• Aliases: None
• Description: SAP30 binding protein [Source:HGNC Symbol;Acc:30785]

Sequence

>retro_mdom_1602
AGCATGAGCAACATTATTGAGGCTTGGAGCAAGATAGCAGCAGTGGGAAAAGGTGGCTTAATATCTTAAATTTATGAAGA
TGATGATTGTTCTTGTCCTCAGGGAAATAGAAATAGTTTTGAGGAAAAGGGTGAATAAAATAGGAGACAATAGGGAGATG
AAGATTCAGAGACTGAAAAACCTGAGGCTGATGACCTAAAGGAGTTTTCATAACTAGAAAAGAGAAAGCCTCAGGAGTTG
GTTGACTCCTTCTCTGAGAGAGTCAGGAACATGTCTCATGATGACATTGAAATTCCCCCTGAACTCCATGGCAGATGCTC
AAGTCTTCTCCAGGACAAAACACAAAAACTATATGAGCAGAAGATAAAGGAAGGGATGGAATTGAATTACATTTTTCAGA
GGAAGAAGGCATTTTGGAATCCCAGCATTTATGAGAAGCTTATCCAATGTTTCAATTGAAATGCTTCACAGCAATTATCC
CAGAGAAATGTTTGACCCCCATGGATGATGATCTGAAGATGCCAACTAT

Alignment

ORF - retro_mdom_1602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.73 %
• Parental protein coverage: 52.07 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEAGVEASGSATAAEEKGGLVSEAYGDDDFSRLEGDEDGYEEEDEENSRQSEDDDSETEKPEADDLKEFS
          S........S..AA..KGGL.S..Y.DDD.S...G.....EE..E.N.RQ..D.DSETEKPEADDLKEFS
Retrocopy SMSNIIEAWSKIAAVGKGGLIS*IYEDDDCSCPQGNRNSFEEKGE*NRRQ*GDEDSETEKPEADDLKEFS

Parental  ELEKRDPQELVASFSERVRNMSPDEITIPPEPPGRCSNHLQDKIQKLYERKIKEGMDMNYIIQRKKEFRN
          .LEKR.PQELV.SFSERVRNMS.D.I.IPPE..GRCS..LQDK.QKLYE.KIKEGM..NYI.QRKK.F.N
Retrocopy *LEKRKPQELVDSFSERVRNMSHDDIEIPPELHGRCSSLLQDKTQKLYEQKIKEGMELNYIFQRKKAFWN

Parental  PSIYEKLIQFC-SIDELGTNYPKDMFDPHG-WSEDSYY
          PSIYEKLIQ.C.SI..L..NYP..MFDPHG..SED..Y
Retrocopy PSIYEKLIQ-C>SIEMLHSNYPREMFDPHG**SEDANY

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_1602 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1602 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ficedula albicollis	ENSFALG00000001071	1 retrocopy	retro_falb_23,
Macropus eugenii	ENSMEUG00000013106	2 retrocopies	retro_meug_1388, retro_meug_1734,
Monodelphis domestica	ENSMODG00000007562	4 retrocopies	retro_mdom_1207, retro_mdom_1211, retro_mdom_1212, retro_mdom_1602 ,
Sarcophilus harrisii	ENSSHAG00000017878	2 retrocopies	retro_shar_19, retro_shar_47,
Taeniopygia guttata	ENSTGUG00000008426	1 retrocopy	retro_tgut_1,
Tarsius syrichta	ENSTSYG00000009667	2 retrocopies	retro_tsyr_175, retro_tsyr_74,