RetrogeneDB ID: retro_mdom_1071

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:502330649..502331366(+)
• Located in intron of: ENSMODG00000023643

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018480
• Aliases: None
• Description: None

Sequence

>retro_mdom_1071
AAAAAGAAAAGGGAAATTACAATCTTCTATCCGGCTTCTATCCAGGCAATGAAAAAAGAGCAAATGTAACAGGAGGATCA
ATGAACACCAAGCAAAAACACAGAAACTCCAGCAAACTGGACACAGGCTTTGGAAGAACTCAAAATACAATTCAAAACAC
AATTAATAGAGGCTGAAGACAATTGAGTAAAGAACGTAAAAATCAAGAAGTCATCTGGAAACAGAGGCACTTGACCTAAA
ATGAGAAAATAGTGTCTTGAAAGCCAATGTTAATCAGCTTGAAAATGAAGCAAAGGAGATGAAAGATCAGAAGGAAAAGA
ATGATCAAAAAGCCAGGGATGAAATTCAGTGGAAACTATGAAACACTTCATTCACAAAACAGAAGATTTAGAAAGTTGGT
CCAGAAGAGATAGCTTAAGAATCATTGGTCTAGTGGAAGACCATGACAAAAGAAAAAGCCTGGATGTCATACTACAGGAA
ATTATTCACAAAAACTGTCCTGACATTCTACAGCAAGAGGGAAAAGTAGAGATTGAAAGAATCCACAGATCACCTCCTGT
ACTTAATCCCCAACTGACAACACCCAGGAATGTTATAGCCAAATTCAAGAACAACCAGATCAAATAAAAAATATTACAAG
TTGCTAAGAAGAAGTCATTCAGATACTATGGAACTACAGTGAGGATAACACAGGAACTGGCTGCTGTTAAGATTAAA

Alignment

ORF - retro_mdom_1071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 72.04 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDKKGTNTLSRAQKNLLEQSKRKQRGRTQQRKKSEIPGNWIQALEELKMQSKTQLREAEDNWEKNL-KTK
          K.K........A...........Q.......K..E.P.NW.QALEELK.Q.KTQL.EAEDN..KN..K..
Retrocopy KKKREITIFYPASIQAMKKEQM*QEDQ*TPSKNTETPANWTQALEELKIQFKTQLIEAEDN*VKNV>KSR

Parental  ISHLETENSVLKAKINQLENEAKEMKDEAKQMKDEVKKMKDDLQRKSDQ-KENMKHLIHKTEDLENRSRR
          .SHLETE...LK.....L.........EAK.MKD..K...D...R...Q..E.MKH.IHKTEDLE..SRR
Retrocopy -SHLETEALDLK*ENSVLKANVNQLENEAKEMKDQ-KEKNDQKARDEIQ<VETMKHFIHKTEDLESWSRR

Parental  DNLRIIGLPEDHDKRKSLDIILQEIIKENCPKILEQEGKVETDRIHRSPPVLNPQLTTPRNVIAKFKDYQ
          D.LRIIGL.EDHDKRKSLD.ILQEII..NCP.IL.QEGKVE..RIHRSPPVLNPQLTTPRNVIAKFK..Q
Retrocopy DSLRIIGLVEDHDKRKSLDVILQEIIHKNCPDILQQEGKVEIERIHRSPPVLNPQLTTPRNVIAKFKNNQ

Parental  I----LQAAKKKSLRYQGTTVRITQDLAASTLK
          I....LQ.AKKKS.RY.GTTVRITQ.LAA...K
Retrocopy IK*KILQVAKKKSFRYYGTTVRITQELAAVKIK

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_1071 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1071 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018480	3 retrocopies	retro_mdom_1071 , retro_mdom_1072, retro_mdom_1346,