RetrogeneDB ID: retro_mdom_1605

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:138836698..138837425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBX1
• Ensembl ID: ENSMODG00000001238
• Aliases: None
• Description: pre-B-cell leukemia homeobox 1 [Source:HGNC Symbol;Acc:8632]

Sequence

>retro_mdom_1605
GCTCAGACAACTAACTCAATTGACCATTCTGACTACAGAGCTAAACCCTCACAAATGCAACAGATCTACCACCAGGGACT
GGAAAAATGTGAACAGGCACGAAGTAAATTCAGCATATGTATGATGAACCTGCTTTGTGAGCAGAGCCAAAACAAACCCA
TCTCACCAAAGGAGAGTGAAAGAATGGTGGTCATCATCTATTGCAAATTCAACTCCATCCAGATGCAACTCAAGCGGAGC
ATACATGAAGTAGTCATGGTGCTTTGCTTGTGGTTTTTGGAAGCAAGGCAGAAGGGATGGAACTTCAAAAGCAAACCACA
AAAATCCTGATTGAGTGTTTCTATTTCCATTTCAGCAACCCTTACCCCAGTAAGGAAGCCAAAGAGGAACTAGCCAAGAA
ATATGGCAGCATGGTCTCACAGGTGTCAAGCTAATTTGAAAATAAGGAAATCCGATACAAGAACATTGGGCAAATTTCAA
GAAGAAACCAATATTTATACTGCCAAAATGGCTGTCACATTTACCAAAGGGTCAGCCCATGCAAGTCAAGCTAACTTACT
CTCAACTTCCAGTTAAGCTCATTCTTTCAGTTCTTTTAATTTTGTCATATGCTAGAGATTTGTTCATGACCATGTAGTCA
GTGGGAATTCTTACTGAGGGGCCCAAGGTGGAACCAGTGGGCAATCACAGGTGGGATGCCCTTTGCTATGTTATCAGCCA
GATAGGG

Alignment

ORF - retro_mdom_1605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.45 %
• Parental protein coverage: 75.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AGSDNSVEHSDYRAKLSQIRQIYHTELEKYEQACNEFTTHVMNLLREQSRTRPISPKEIERMVSIIHRKF
          A...NS..HSDYRAK.SQ..QIYH..LEK.EQA...F....MNLL.EQS...PISPKE.ERMV.II..KF
Retrocopy AQTTNSIDHSDYRAKPSQMQQIYHQGLEKCEQARSKFSICMMNLLCEQSQNKPISPKESERMVVIIYCKF

Parental  SSIQMQLKQSTCEAVMILRSRFLDARRKRRNF-NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITV
          .SIQMQLK.S..E.VM.L...FL.AR.K..NF..KQ.T.IL.E.FY.H.SNPYPS.EAKEELAKK.G..V
Retrocopy NSIQMQLKRSIHEVVMVLCLWFLEARQKGWNF<QKQTTKILIECFYFHFSNPYPSKEAKEELAKKYGSMV

Parental  SQVSNWFGNKRIRYKKNI-GKFQEEANIYAAKTAVTATNVSAHGSQANSPSTPNSAGSSSSFN-MSNSGD
          SQVS..F.NK.IRY.KNI.GKFQEE.NIY.AK.AVT.T..SAH.SQAN..ST...A.S.SSFN..S...D
Retrocopy SQVSS*FENKEIRY-KNI>GKFQEETNIYTAKMAVTFTKGSAHASQANLLSTSS*AHSFSSFN>LSYARD

Parental  LFMSVQSLNGDSYQGAQV-GANVQSQV-DTLRHVISQTG
          LFM...S..G....G..V.G...QSQV.D.L..VISQ.G
Retrocopy LFMTM*SV-GILTEGPKV<GTSGQSQV>DALCYVISQIG

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_1605 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1605 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001238	1 retrocopy	retro_mdom_1605 ,
Procavia capensis	ENSPCAG00000002628	1 retrocopy	retro_pcap_310,
Sarcophilus harrisii	ENSSHAG00000012750	1 retrocopy	retro_shar_377,
Tarsius syrichta	ENSTSYG00000012332	3 retrocopies	retro_tsyr_1980, retro_tsyr_479, retro_tsyr_723,