RetrogeneDB ID: retro_mdom_731

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:254514839..254515579(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DHPS
• Ensembl ID: ENSMODG00000006807
• Aliases: None
• Description: deoxyhypusine synthase [Source:HGNC Symbol;Acc:2869]

Sequence

>retro_mdom_731
CTTCTATCCTTAGGCACAGTTCTGCCCACTGAAGCCATCCAGGTCCAGGGCTACGACTTCAACCACAGCCTGGATTATGG
TATTCTCCTGCGTGCCATGGGCACTACAGGCTTCTAAGTCACTAGCTTCAGATAAGTAGTGCACCAGGTCAGTGCCATGA
TTGAGAAGAAGCTGGAGAGGGGAGGTGGAGGAGGAGAACCACATGGACCTAAATCCAAGCCCTCAATGAGTCGCTGCACT
ATATTCTTCGGCTACACATCAAATCTAATCAGCTCTGGTGTCAGAGAGACTGTATGTTACCTGGTGCAGCACAACATGAT
GGATGTTCTGGTGACAACTGCAGGTGGTATGGAGGAGGATCTGGTCAAAAACTTTGCATCTACATATCTGGGAGAATTTA
GCCTGAATTGGAAGGACCTGAGACAAAATAGCATCAACAGGTTGAGAAACCTACTTGACCCAATGACAATTATTGCAAGT
TTGAGAACTGGCTGATGCTGATTTTGAATCAGATGGTTCTGGAGCAAAATACAGAGGGAGTGAAATGGACTCCATCGAAG
ATGATTGCTCGACTGAGTAAAGAACTCAACAACCTGGAGTCTGTGTATTACTGGGCACAGAAGAACAATATCCCAGTGCT
AAGCCCAGCTCTGACAGATGGCTCTCTTGGTGATATAATATTCTTCCACTCATTTAAGAACCTTGGGCTGGTGCTGGAAA
TCATGGAGGACTTACGACTA

Alignment

ORF - retro_mdom_731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.5 %
• Parental protein coverage: 67.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLRHSSALPAGTVQVRGYDFNRGLDYGALLRAFGTTGFQATSFGRAVQQVNAMIEKKLEPLGEEEENHMD
          .L.....LP....QV.GYDFN..LDYG.LLRA.GTTGF..TSF...V.QV.AMIEKKLE..G...E.H..
Retrocopy LLSLGTVLPTEAIQVQGYDFNHSLDYGILLRAMGTTGF*VTSFR*VVHQVSAMIEKKLERGGGGGEPH--

Parental  LNPSRRP-MSGCTIFLGYTSNLISSGVRETIRYLVQHNMVDVLVTTAGGIEEDLIKCLAPTYLGEFSLKG
          ..P...P.MS.CTIF.GYTSNLISSGVRET..YLVQHNM.DVLVTTAGG.EEDL.K..A.TYLGEFSL..
Retrocopy -GPKSKPSMSRCTIFFGYTSNLISSGVRETVCYLVQHNMMDVLVTTAGGMEEDLVKNFASTYLGEFSLNW

Parental  KDLRQNGINRIGNLLVP-NDNYCKFEDWLMPILDQMVLEQNTEGVKWTPSKMIARLGKEINNPESVYYWA
          KDLRQN.INR..NLL.P.NDNYCKFE.WLM.IL.QMVLEQNTEGVKWTPSKMIARL.KE.NN.ESVYYWA
Retrocopy KDLRQNSINRLRNLLDP<NDNYCKFENWLMLILNQMVLEQNTEGVKWTPSKMIARLSKELNNLESVYYWA

Parental  QKNNIPVLSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRL
          QKNNIPVLSPALTDGSLGD.IFFHS.KN.GLVL.I.EDLRL
Retrocopy QKNNIPVLSPALTDGSLGDIIFFHSFKNLGLVLEIMEDLRL

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_731 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_731 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000000465	1 retrocopy	retro_fcat_1573,
Monodelphis domestica	ENSMODG00000006807	2 retrocopies	retro_mdom_731 , retro_mdom_753,
Sarcophilus harrisii	ENSSHAG00000015920	1 retrocopy	retro_shar_774,