RetrogeneDB ID: retro_mdom_1103

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:117816941..117817683(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD1
• Ensembl ID: ENSMODG00000020640
• Aliases: None
• Description: OCIA domain containing 1 [Source:HGNC Symbol;Acc:16074]

Sequence

>retro_mdom_1103
GGAAAGATGTATAGAAGGATAGATTTTGGAACAGAGCATAATGCAGAGGTCTCACCACTACTCCCTAACATAGGAACAGA
TTACATTACAACAGAAGAGGAAAGGAGAGCCTTCACTAAATGTAATCAAGAGAACTTCTGGTACAGATATCTTCTGTTTT
CTGCATCAAGTATGTTGGTTACTCACGGATTAGTTGCTAAAAGAATTCTTTCCAGTCACCCCAAATATGGTTCTGTTCCT
AAACTTGTATTTGCTTGTGTAATGGGATACGTAGATGGAAAAATTCTTATGTGAAAACTTGTCAAGAGAAATTTAAAGGG
CTTGAAAATTCTCCTCTTGGTGAAGCTCTGCATCTGAGACAGGGAGCTTGACTTGGATCACCTGGATATCTTTCACAAAA
GTCAGGATTTGCGCCTGCACCTTCATCTATTCAAGCATCCCCCACATCTGAAAAAAAATGAAAAAGTTCCTTTCCTCTTT
ATGAACCAGTCTGCTTCAGTGCTTCCTTGAATGAATCAACTCCTACTGGTATCACTGATTATAATGCCCAAGGATCTGAT
ACAAGCATAGAAGAAAATATTTCTAAGAAAAAAATTTGTTACATATGAAGAATTAAGGAATAAGAATAGAGAAATATATG
AGGTTTCCTTGCCACAAAAAAGTGACACCCCACTTAAGTCTATGCATGAAAGAACACCAAAAAATAGGGAAAGTAAATCA
ATATGCAGATACTTGGGATGAG

Alignment

ORF - retro_mdom_1103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.24 %
• Parental protein coverage: 94.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GKMNGRTDFGTEQNAEVSPPLPNIGMDYIPTEEERRAFIECNQESFWYRSLPFSATSMLVTQGLIAKGIL
          GKM..R.DFGTE.NAEVSP.LPNIG.DYI.TEEERRAF..CNQE.FWYR.L.FSA.SMLVT.GL.AK.IL
Retrocopy GKMYRRIDFGTEHNAEVSPLLPNIGTDYITTEEERRAFTKCNQENFWYRYLLFSASSMLVTHGLVAKRIL

Parental  SSHPKYGSVPKLVFACVMGYLAGKI-SYVKTCQEKFKRLENSPLGEALRLGQGARFGSPGYLSQKSEFEP
          SSHPKYGSVPKLVFACVMGY..GKI.SYVKTCQEKFK.LENSPLGEAL.L.QGA..GSPGYLSQKS.F.P
Retrocopy SSHPKYGSVPKLVFACVMGYVDGKI<SYVKTCQEKFKGLENSPLGEALHLRQGA*LGSPGYLSQKSGFAP

Parental  APTSIGASPTSEKSEKESSFPLYEPVPFSASLNESTPTGITDYNAQGPDTSIEENLSKKKV-VTYEELRN
          AP.SI.ASPTS.......SFPLYEPV.FSASLNESTPTGITDYNAQG.DTSIEEN.SKKK..VTYEELRN
Retrocopy APSSIQASPTS-XXXXXXSFPLYEPVCFSASLNESTPTGITDYNAQGSDTSIEENISKKKI>VTYEELRN

Parental  KNRETYEVALSQKSDTPLKPIQERTP-KKQGK-VNQYGDTWDE
          KNRE.YEV.L.QKSDTPLK...ERTP.KK.GK.VNQY.DTWDE
Retrocopy KNREIYEVSLPQKSDTPLKSMHERTP<KK*GK<VNQYADTWDE

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_1103 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1103 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011863	1 retrocopy	retro_cpor_928,
Echinops telfairi	ENSETEG00000005961	1 retrocopy	retro_etel_1731,
Latimeria chalumnae	ENSLACG00000014002	1 retrocopy	retro_lcha_88,
Macropus eugenii	ENSMEUG00000010655	2 retrocopies	retro_meug_1692, retro_meug_2016,
Monodelphis domestica	ENSMODG00000020640	1 retrocopy	retro_mdom_1103 ,
Monodelphis domestica	ENSMODG00000025531	1 retrocopy	retro_mdom_1006,
Sarcophilus harrisii	ENSSHAG00000018132	1 retrocopy	retro_shar_74,
Ictidomys tridecemlineatus	ENSSTOG00000014963	1 retrocopy	retro_itri_986,