RetrogeneDB ID: retro_mdom_915

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:418390883..418392047(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EHD3
• Ensembl ID: ENSMODG00000015505
• Aliases: None
• Description: EH-domain containing 3 [Source:HGNC Symbol;Acc:3244]

Sequence

>retro_mdom_915
AAGGGTTCCTATCTTTTTTTATCAGTGGCTCAGAGATTGAGTAAACTGTACTTGGAAAAGCTGCTGCCATTGGAAGAGAT
GTATCAGTTTGGTAGGTTCCACTCGCCTCCACTCACGGACGCAGACTTCGATAACCGGCCCATGGTGCTTCTGATGGGCC
AGTACAGCACAGGGAAGACAACCTTCATCAGTCACCTCATCGAGCAGACATTCCCGTGCATGCGCATTGGACCCGAGCCC
ACTACTGATGCCTTCATTGTCCTCATGCATGGTGAAGTGGAGAACGTGATGCCAGGAAACGTGGCTGTGGTAGACCGACG
CTTCCCCTTCCGCAATCTCACCAGATTTGGCAATGCCTTTCTCAATCGCTTCAATTTGGTCCAGATACCCAATGAGTTTC
TGGACAGTATCAGCATCATTGACACCCCTGGAATTCTTGCTGGTGAGAAACAACGGCTCAGTAGAGGTTATGACTTCTCA
GCAGTGCTCGAGTGGTTTGCCCAGCGGGTAGATCTTATCATCCTGCTTTTTGATGCTCATAAATTGGACATATCCGATGA
ACTGTCCCAGGCAATCAAATCTATCAAGAACAATGAAGATAAAATGCGAGTAGTGCTAAACAAATCTGACCAGGTGGGAA
CTCAGCAACTGATGCGGGTCTATGGGGCCCTCATGTGGTCCTTGGGCAAGATCATTAATACCCCCGAGGTGATGAGGGTG
TATATAGGTTCCTTCTGGTCAGAGCCCTATGTGAATGATGAAAACAGCAAGCTTTTTGAAGCAGAGGCTTTGGATCTTTA
TAAGGACATTCAGCAGCTGCCCCATTATAGTACTGTTAGGAAAATGAATGACCTGATCAAACGAGCCAGGTTGGCCAGGG
TCCATGGCTACATCATCGCCACCCTCAAGAAAGAGTTGCCCTTATTTGGGAAGGAGAACAAAAAAAGGGAATTGATCACC
AACCTACAAGAGATCTTCCTTAAAGTTCAACGAGATTATCATATTTCTTCTGGAGACTTCCCAAATGTCCAGAAAATGCA
AGAAATACTAGTTTCCCAAGACTTCACCAAGTTCCAGAATCTGAAACCCAAGCTCTTTGATACATTGGAAGACATGCTGT
CAAAAGATATAACTCGTTTGATGTATTTGATGAGAGAAGAAGAG

Alignment

ORF - retro_mdom_915 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.12 %
• Parental protein coverage: 72.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDPEVFQTVSEGLKKLYKTKLLPLEEYYRFHEFHSPALEDADFDNKPMVLLVGQYSTGKTTFIRYLLEQD
          K....F..V...L.KLY..KLLPLEE.Y.F..FHSP.L.DADFDN.PMVLL.GQYSTGKTTFI..L.EQ.
Retrocopy KGSYLFLSVAQRLSKLYLEKLLPLEEMYQFGRFHSPPLTDADFDNRPMVLLMGQYSTGKTTFISHLIEQT

Parental  FPGMRIGPEPTTDSFIAVMQGDVEGIIPGNALVVDPKKPFRKLNAFGNAFLNRFVCAQLPNPVLESISVI
          FP.MRIGPEPTTD.FI..M.G.VE...PGN..VVD...PFR.L..FGNAFLNRF...Q.PN..L.SIS.I
Retrocopy FPCMRIGPEPTTDAFIVLMHGEVENVMPGNVAVVDRRFPFRNLTRFGNAFLNRFNLVQIPNEFLDSISII

Parental  DTPGILSGEKQRISRGYDFAAVLEWFAERVDRIILLFDAHKLDISDEFSEVIKALKNHEDKMRVVLNKAD
          DTPGIL.GEKQR.SRGYDF.AVLEWFA.RVD.IILLFDAHKLDISDE.S..IK..KN.EDKMRVVLNK.D
Retrocopy DTPGILAGEKQRLSRGYDFSAVLEWFAQRVDLIILLFDAHKLDISDELSQAIKSIKNNEDKMRVVLNKSD

Parental  QIETQQLMRVYGALMWSLGKIVNTPEVIRVYIGSFWSHPLLIPDNRKLFEAEEQDLFRDIQSLPRNAALR
          Q..TQQLMRVYGALMWSLGKI.NTPEV.RVYIGSFWS.P.....N.KLFEAE..DL..DIQ.LP.....R
Retrocopy QVGTQQLMRVYGALMWSLGKIINTPEVMRVYIGSFWSEPYVNDENSKLFEAEALDLYKDIQQLPHYSTVR

Parental  KLNDLIKRARLAKVHAYIISSLKKEMPSVFGKDNKKKELVNNLGEIYGRIEREHQISPGDFPNLKKMQDQ
          K.NDLIKRARLA.VH.YII..LKKE.P..FGK.NKK.EL..NL.EI.....R...IS.GDFPN..KMQ..
Retrocopy KMNDLIKRARLARVHGYIIATLKKELP-LFGKENKKRELITNLQEIFLKVQRDYHISSGDFPNVQKMQEI

Parental  LQAQDFSKFQPLKNKLLEVVEDMLAHDIAQLMVLVRQEE
          L..QDF.KFQ.LK.KL....EDML..DI..LM.L.R.EE
Retrocopy LVSQDFTKFQNLKPKLFDTLEDMLSKDITRLMYLMREEE

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	600.39 RPM
SRP007412_cerebellum	0.00 RPM	290.54 RPM
SRP007412_heart	0.00 RPM	425.82 RPM
SRP007412_kidney	0.00 RPM	529.37 RPM
SRP007412_liver	0.00 RPM	448.61 RPM
SRP007412_testis	0.00 RPM	118.65 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_915 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_915 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015195	1 retrocopy	retro_ecab_581,
Monodelphis domestica	ENSMODG00000015505	1 retrocopy	retro_mdom_915 ,
Sarcophilus harrisii	ENSSHAG00000013011	1 retrocopy	retro_shar_114,
Tupaia belangeri	ENSTBEG00000010371	1 retrocopy	retro_tbel_4556,