RetrogeneDB ID: retro_mdom_1252

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:106794502..106795257(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GULP1
• Ensembl ID: ENSMODG00000010712
• Aliases: None
• Description: GULP, engulfment adaptor PTB domain containing 1 [Source:HGNC Symbol;Acc:18649]

Sequence

>retro_mdom_1252
AATGCAAAGTTTCTTGGCAGTACAGAATGGAGCAGCCCAAAGATACTGTAGTTACCAGAGATGCAGTTAGAAAACTGAAG
TTTGTAAGACATATCAAGAAATCTGAACGTCAAAAAATTTCAAAAGTTGAATTGTAAATATCAATTTATGGGGTAAAAAT
TCTAGAATCAAAACCAAAGGAAGTCTAGCACAATTGCCAGCTTCATAGGTTAGAATTTTGTTCAGATGATAAAACTGACA
AGAGGATATTTACTTTCATATGCAAAAATTCTGAGTCAAATAAGCACTTTGCTATGTCTTTGATAATGAAAAGTGTGCTG
AAGAGATCATTTTAACTATTGGTCAAGCAATTGATCTGGCCCACAGGAAGTTTCTAGAATATGGGGGAAAAGATGTTGAA
ACAAGGAAACAGATTGCAGGGTTGCAGAAAAGATTTTGCAAGAACTAGAAAGTGAGAACCTAGAACTCAGAAATAGAGTC
CAGAACTTGGAAAGCCAGCTAAGAATAACTCAGCTATCAACATCTCTAGCATCCAGTGTGACACCCAAATCACCTTCCAC
TGAAATCTTCATGGTTCCTTTTCCTCCAATAACTCCTCACTTATCAACACCAACTTGCAATGGTACATAGCTTCCTCTAC
CAGTTGATCTACAGAGATAAAAAGAGACCTTTTTGGAGCAGAATTTTTTGATCCCTTTACCTGTGGAGCAGGTGACTTCC
CTCCAGACATTCAATCAAAACTAGATGAGATGCAG

Alignment

ORF - retro_mdom_1252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.45 %
• Parental protein coverage: 95.13 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  NFQFLGSTE-VEQPKGTEVVRDAVRKLKFARHIKKSEGQKTPKVELQISIYGVKILEPKTKEVQHNCQLH
          N..FLGSTE..EQPK.T.V.RDAVRKLKF.RHIKKSE.QK..KVEL.ISIYGVKILE.K.KEV.HNCQLH
Retrocopy NAKFLGSTE<MEQPKDTVVTRDAVRKLKFVRHIKKSERQKISKVEL*ISIYGVKILESKPKEV*HNCQLH

Parental  RISFCADDKTDKRIFTFICKDSESNKH-LCYVFDSEKCAEEITLTIGQAFDLAYRKFLE-SGGKDVETRK
          R..FC.DDKTDKRIFTFICK.SESNKH.LCYVFD.EKCAEEI.LTIGQA.DLA.RKFLE..G.K......
Retrocopy RLEFCSDDKTDKRIFTFICKNSESNKH<LCYVFDNEKCAEEIILTIGQAIDLAHRKFLE>MGEKMLKQGN

Parental  QIAGLQKR-IQELETENIELRNKVQDLENQLRITQISTSPASSVTPKSPSTDIFDMVPFSPITPQLSTPT
          ...G..K...QELE.EN.ELRN.VQ.LE.QLRITQ.STS.ASSVTPKSPST.IF.MVPF.PITP.LSTPT
Retrocopy RLQGCRKD>LQELESENLELRNRVQNLESQLRITQLSTSLASSVTPKSPSTEIF-MVPFPPITPHLSTPT

Parental  RNGTQPPPVP-SRSTEIKRDLFGAEPFDPFNCGAGDFPPDIQSKLDEMQ
          .NGT...P.P.S.STEIKRDLFGAE.FDPF.CGAGDFPPDIQSKLDEMQ
Retrocopy CNGT-*LPLP<S*STEIKRDLFGAEFFDPFTCGAGDFPPDIQSKLDEMQ

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_1252 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1252 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010712	1 retrocopy	retro_mdom_1252 ,
Mustela putorius furo	ENSMPUG00000012293	1 retrocopy	retro_mputfur_1040,