RetrogeneDB ID: retro_mdom_1977

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:34231483..34232389(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000016527
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FOXN2
• Ensembl ID: ENSMODG00000001169
• Aliases: None
• Description: forkhead box N2 [Source:HGNC Symbol;Acc:5281]

Sequence

>retro_mdom_1977
GCCGAAACTCTTGCAGGATTAAGCCAGATTTACAGAATGGGAAGTTTGCTTGAAGCAGTTGATGCTGCCAGGCCAAAAGC
TACTTTAGTGGATGGCGAATCAGCAAATGATGAGCTTCCAAACTTGAACTGGCTTCATGAAAGTACTAATCTTCTAACAA
ACGTCAGCCTTGGAAGTGAAGGTCTTCCTATTGTTAGTCCAATGTATGACATTGAGGGCGATGATGTGCCATCTTTTGTA
CCATCTTACCAGAACACAGAAAAAGGTCAGGGAATTCCAAAGCCCCTTACTCCTTAGTCTTCGCATTTCTATGACTATTG
AACATTCTCCAAATAAATGCCTGCCAGTCAAAGAGATCTACAGCGGGATTTGGGAACGCTTTCCATGTTTTGTTATGGCA
CCAACAGGTTGGGAGAATTCCATCAGACACAACCTTTCATTGAATAAATGTTTTCAGAAAGTGGAGAGCAGTCGTGGCAA
GGTGAATGGAAAAGGTTCCTTATGGTGCGTTGATCCAGAATATAAACCCATCCTTCTACAAGCACTGAAGAAGCAGCCTT
TTCCCTCAGCACTTCATTTTACAGCCCTCCTGCATTGCCACAAAATGGATCGTCACCACCTCATTCTATAACCTCTGTAC
TAATTCGGCAGAGTGGAGTTCGAACTCTGAAAGAATCTGATATTGATGCAGCCACTGCAATGATGCTTTTAAATACATCG
ACTGAACAAGGAAGTTTAGAATGTGAGAAGCCACTGCCACTCCAAACAGCTTTGCAAAGGAAAAGGAGTTTTGTTCGTGC
ATTTAACCATCCCAGTGCCATGGATTGACAAGAGGATGATTGTGCAGTCAACAATATGGAGTCAAAGGAGGACCACAATT
ACAGCGCAAGCAGCAGCGCGATTCAG

Alignment

ORF - retro_mdom_1977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.68 %
• Parental protein coverage: 69.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AEKVAGLSQIYRMGSLPEAVDAARPKATLVDSESADDELTNLNWLHESTNLLTNFSLGSEGLPIVSPIYD
          AE..AGLSQIYRMGSL.EAVDAARPKATLVD.ESA.DEL.NLNWLHESTNLLTN.SLGSEGLPIVSP.YD
Retrocopy AETLAGLSQIYRMGSLLEAVDAARPKATLVDGESANDELPNLNWLHESTNLLTNVSLGSEGLPIVSPMYD

Parental  IEGDNVPSFVPSYQNTEK-KSGNSKPPYSF-SLLIYMAIEHSPNKCLPVKEIYSWILERFPYFATAPTGW
          IEGD.VPSFVPSYQNTEK..SGNSK.PYS..SL.I.M.IEHSPNKCLPVKEIYS.I.ERFP.F..APTGW
Retrocopy IEGDDVPSFVPSYQNTEK<RSGNSKAPYSL<SLRISMTIEHSPNKCLPVKEIYSGIWERFPCFVMAPTGW

Parental  KNSVRHNLSLNKCFQKVERSHGKVNGKGSLWCVDPEYKPNLIQALKKQPFSSAL-AFYTPPASPQNGSSP
          .NS.RHNLSLNKCFQKVE.S.GKVNGKGSLWCVDPEYKP.L.QALKKQPF.SAL..FY.PPA.PQNGSSP
Retrocopy ENSIRHNLSLNKCFQKVESSRGKVNGKGSLWCVDPEYKPILLQALKKQPFPSAL<SFYSPPALPQNGSSP

Parental  PHYITSVL-KQSQVRTLKESDIDAATAMMLLNTSIEQGILECEKPLPLKTALQKKRSFVSAFTHPSAINL
          PH.ITSVL..QS.VRTLKESDIDAATAMMLLNTS.EQG.LECEKPLPL.TALQ.KRSFV.AF.HPSA...
Retrocopy PHSITSVLIRQSGVRTLKESDIDAATAMMLLNTSTEQGSLECEKPLPLQTALQRKRSFVRAFNHPSAMD*

Parental  QENDSAVNNIDPKEDHNYSASSIATQ
          QE.D.AVNN...KEDHNYSASS.A.Q
Retrocopy QEDDCAVNNMESKEDHNYSASSSAIQ

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	31.71 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	17.29 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1977 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1977 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	ENSMODG00000001169	1 retrocopy	retro_mdom_1977 ,
Mus musculus	ENSMUSG00000034998	1 retrocopy	retro_mmus_3189,