RetrogeneDB ID: retro_mdom_1278

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:252645123..252646073(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK5RAP1
• Ensembl ID: ENSMODG00000000175
• Aliases: None
• Description: CDK5 regulatory subunit associated protein 1 [Source:HGNC Symbol;Acc:15880]

Sequence

>retro_mdom_1278
ATGCAGCCTTTAAAATGTGCATTGAGAACAGGTCAGACTCTGAGGTAGAGTCCATTGTCTTCAGTAATCAGGCAAATACT
CAGGACCTACAGAACAACAAGCCATCTCAATGCAGAAGTGTACCCAGAGTTAGAAAAACAGCAAGATGATAGACTCCAGA
GAGATTTCAGCTCTAGACTGGCAGCAGGACCAACATTTCAGCACTTTCTAAGAAATGCCTCTGTTCCTCAAGAGAAGTCT
GATTCCTCTGCAACAGTGGAGCATCCACCACCTTATCTTACTCCAGAAGCCCTTTTAGGAAGAGGGAGAAAAGTCTACCT
ACAGACTTTTGGTTGCCAAATGAATGTTAATGATGCAGAGATTGCTTGGGCCATTCTTTAGAAGAGTGGCTACTTGAGAA
CTAACACTGTCCACGAGGCTGACGTGATTCTTCTTGTCACATGTTCAATAAGGGAAAAGGCTGAACAGGCTATTTGTAAT
TCTTTAAAATGACTTAAATCTGTAAAGGCCAGACATCTCAGATCACAAGTTCCCCTTTGAATTAGGATTCTAGGTATCCT
AAAGTTTGGATATATGGCTGAAAGGTTGAAGGAAGAGATGCTGCACAGGAAAAATTGGTGGATATTGTAGCTGGACCAGA
TACTTACCAGAATCTTCCTCGGCCGCTGTCTTTGGCTTATTCTGGACAGCAATTTGCTAATGTTTTGCTTTCACTAGAGG
AGACCTATGCAGACATCATGCCAGTCCAGACAAGTTCAAATGCCACATCAGCATTTGTGTCAATTTTGCGAGGTTGTGAT
AACATGTGTAGCTACTGTATTGTTCCTTTCACACGTGGCCATGAAAGAAGTTGGCCAATTGCCTCCATTCTGGAAGAAGT
AAAGAAACTCTCTCAGCAGGGCCTTAAAGAAGTAACACTCATTGGTCAGAATGTCAATAGCTATTGAGAC

Alignment

ORF - retro_mdom_1278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.99 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQPLKCALRTGQTLRQSPLSSVIGQILRTYRTTNHLNAEVYPELEKQQDDRLQRDFSSRLAAGPTFQHFL
          MQPLKCALRTGQTLR.SPLSSVI.QILRTYRTT.HLNAEVYPELEKQQDDRLQRDFSSRLAAGPTFQHFL
Retrocopy MQPLKCALRTGQTLR*SPLSSVIRQILRTYRTTSHLNAEVYPELEKQQDDRLQRDFSSRLAAGPTFQHFL

Parental  RNASVPQEKSDSSATVEDPPPYLTPEALLGRGRKVYLETYGCQMNVNDAEIAWAILQKSGYLRTNTLHEA
          RNASVPQEKSDSSATVE.PPPYLTPEALLGRGRKVYL.T.GCQMNVNDAEIAWAIL.KSGYLRTNT.HEA
Retrocopy RNASVPQEKSDSSATVEHPPPYLTPEALLGRGRKVYLQTFGCQMNVNDAEIAWAIL*KSGYLRTNTVHEA

Parental  DVILLVTCSIREKAEQAIWNRLKRLKFIKARRLRSQVPLRI---GIL--GCMAERLKEEILHR-EKLVDI
          DVILLVTCSIREKAEQAI.N.LK.LK..KAR.LRSQVPL.I...GIL..G.MAERLKEE.LHR.EKLVDI
Retrocopy DVILLVTCSIREKAEQAICNSLK*LKSVKARHLRSQVPL*IRILGILKFGYMAERLKEEMLHR<EKLVDI

Parental  VAGPDAYRDLPRLLSLADSGQRSANVLLSLEETYADIMPVQTSSNATSAFVSIMRGCDNMCSYCIVPFTR
          VAGPD.Y..LPR.LSLA.SGQ..ANVLLSLEETYADIMPVQTSSNATSAFVSI.RGCDNMCSYCIVPFTR
Retrocopy VAGPDTYQNLPRPLSLAYSGQQFANVLLSLEETYADIMPVQTSSNATSAFVSILRGCDNMCSYCIVPFTR

Parental  GRERSRPIASILEEVKKLSQQGLKEVTLLGQNVNSYQD
          G.ERS.PIASILEEVKKLSQQGLKEVTL.GQNVNSY.D
Retrocopy GHERSWPIASILEEVKKLSQQGLKEVTLIGQNVNSY*D

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	41.12 RPM
SRP007412_cerebellum	0.00 RPM	56.15 RPM
SRP007412_heart	0.00 RPM	88.31 RPM
SRP007412_kidney	0.00 RPM	77.69 RPM
SRP007412_liver	0.00 RPM	52.87 RPM
SRP007412_testis	0.00 RPM	31.63 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1278 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1278 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000000175	1 retrocopy	retro_mdom_1278 ,