RetrogeneDB ID: retro_mdom_1959

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:30144804..30145950(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006247
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BSPRY
• Ensembl ID: ENSMODG00000004402
• Aliases: None
• Description: B-box and SPRY domain containing [Source:HGNC Symbol;Acc:18232]

Sequence

>retro_mdom_1959
GACCAAGCGCCACGATGTCCCGAGCATGACCTGGAGCTGAAATGGTTCTGCAGCGCCGAGGGGCCTGTTGTGTGCACCAG
CTGCAAGGGTCTGGGGGGGCCCTGCCGAGAGCACCATGTCCGGAGGGAGGAGGAGCGGGCAGAGGAGTTGCAGAACAAGG
TCCTGGATCAGTGTGAGAAGCTGCAGCTACAGAGTGCTGGCATCACCAAATAAATGGCTGAAGTCTTGCTTCGGAAAAAC
CAAAATGCAGCGACCTTAGCCAGTGGGGCCCGGGAGATAGTGATCCAGCGGCTGGGCCTGGTGAAGAATGTGTGTGAGAG
TGAGGAGCAGAGGCTGCTGGAACAGGTTCACAGGGAGGAGGAGCGAGCCCACCAGAGCATCCTGACCCAGCGATCCATTG
GACCGAGGCCTTACAGAAGCTCAGCACCAACCTAGTGAGCATGCTCACTGATCTGGATGACCTCAGCCTTGTTCAATCAG
TGGGGAGATTTTTGAGAGGACTGAGGAAGCTGAGGGAGTCTTGGATCTCCAGGAATCTGAGAAGTTACATTTTAATCAGA
AATGTGTTTGGAGCCCATTATTGACCCAGCTCTGGGCATCGGCTGTTCTCTGCTGTCTATCAGGTACTGAGGACATGCAG
GTGGATGAGAGGACCATCAGTCCCTTTCTCCGACTGTCAGAGGACAGGAAGACCTTAACCTTCAGTGCCAAGAAGTCTAA
GGCCTATGCAGATGGCCCGGAACCCTTTGACCACTGGCCCAATGCCCTGGCTTCAACCTCCTTCCAGGGTGGCCTTCGTG
CCCGGATAGTGAATGTAGAGAACAGCTGTGCCCATAAGGTGGGAGTCTCCTCGAGCCAGCTGCCCCAAAAGGGTTCTGGC
AGTGACACCCGCCTTGGCCACAATGCTTCTTCCTGGGTTTTCTCTCGCTATGACCAGGAATTCCGGTTCCTGCACTATGG
TCAGTACCAGCCTTTGGCGCTGCTGCACTGGCCAGACTGCATTGGGGTGTGTTGGACTTGGCAGTGGGCGAGCTGCTGTT
CTATGAGCCCACCTCAGGGACCCTCTCGTGTTCCTGCCATGCCCAGTTGGAGGGCCCTATCTTTCCCATCTTTGCTGTGG
CTGACCAGAACATCTCCATTGTTCAG

Alignment

ORF - retro_mdom_1959 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.92 %
• Parental protein coverage: 96.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DSAPRCPEHDLELKWFCSSERRLVCASCKGLGGPCREHHVRRAEERAEELRNKIVDQCEKLQLQSAGITK
          D.APRCPEHDLELKWFCS.E...VC.SCKGLGGPCREHHVRR.EERAEEL.NK..DQCEKLQLQSAGITK
Retrocopy DQAPRCPEHDLELKWFCSAEGPVVCTSCKGLGGPCREHHVRREEERAEELQNKVLDQCEKLQLQSAGITK

Parental  YMAEVLPRKNQNAATLASGAREIVIQRLGLVKNVCESEEQRLLEQVHTEEERAHQSILTQRS-HWTEALQ
          .MAEVL.RKNQNAATLASGAREIVIQRLGLVKNVCESEEQRLLEQVH.EEERAHQSILTQRS.HWTEALQ
Retrocopy *MAEVLLRKNQNAATLASGAREIVIQRLGLVKNVCESEEQRLLEQVHREEERAHQSILTQRS<HWTEALQ

Parental  KLSTIRTNLVSMLTDLDDRSLVQS-EREIFERTEEAEGILDPQESEKLNFNQKCVRSPLLTQLWASAVLC
          KLS...TNLVSMLTDLDD.SLVQS...EIFERTEEAEG.LD.QESEKL.FNQKCV.SPLLTQLWASAVLC
Retrocopy KLS---TNLVSMLTDLDDLSLVQS<SGEIFERTEEAEGVLDLQESEKLHFNQKCVWSPLLTQLWASAVLC

Parental  CLSGTEDIQVDERTISPFLRLSEDRKTLTFNPKKSKAYADGPERFDHWPNALASTSFQGGLHAWIVNVEN
          CLSGTED.QVDERTISPFLRLSEDRKTLTF..KKSKAYADGPE.FDHWPNALASTSFQGGL.A.IVNVEN
Retrocopy CLSGTEDMQVDERTISPFLRLSEDRKTLTFSAKKSKAYADGPEPFDHWPNALASTSFQGGLRARIVNVEN

Parental  SCAYKVGVSSSQLPRKGSGSDTRLGHNAFSWVFSRYDQEFRFLHCGQYQPLALLRCPDRIGV-LLDLAAG
          SCA.KVGVSSSQLP.KGSGSDTRLGHNA.SWVFSRYDQEFRFLH.GQYQPLALL..PD.IGV..LDLA.G
Retrocopy SCAHKVGVSSSQLPQKGSGSDTRLGHNASSWVFSRYDQEFRFLHYGQYQPLALLHWPDCIGV<VLDLAVG

Parental  ELLFYEPTSGALLCSYHAQFEGPIFPVFAVADQKISIVQ
          ELLFYEPTSG.L.CS.HAQ.EGPIFP.FAVADQ.ISIVQ
Retrocopy ELLFYEPTSGTLSCSCHAQLEGPIFPIFAVADQNISIVQ

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	108.83 RPM
SRP007412_cerebellum	0.00 RPM	25.79 RPM
SRP007412_heart	0.00 RPM	8.37 RPM
SRP007412_kidney	0.00 RPM	38.19 RPM
SRP007412_liver	0.00 RPM	2.01 RPM
SRP007412_testis	0.00 RPM	8.84 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1959 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1959 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	ENSMODG00000004402	1 retrocopy	retro_mdom_1959 ,
Tupaia belangeri	ENSTBEG00000003560	1 retrocopy	retro_tbel_2089,