RetrogeneDB ID: retro_mdom_235

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:10978140..10979598(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000022847
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000006919
• Aliases: None
• Description: None

Sequence

>retro_mdom_235
ACTGACTACCAAAGGTTGTGTCTAACCCCGGCAGGACCCAGGGAGCAGAATCCAAGAAATCCGACTAGTGTGAAAGCCAA
GATGAGCTGGAGTCTGACGCCATTCAGTTTTCCAGTGTCCTCTCATGGCAAACACGGGGACCGCTACATTCCCTCCCGAG
CTGGAGCTAATTGGAACCTCCACTTCCACAGCACAGCTGACACTGATAATTCCCCAGGGCAGAAACAGAAAGAGGATACC
TGGGGCAATGGCCAAGATGCCTCAGTCTATTCTACCTTGTTGAAGAATGAGCTCCTGGAAGCCAAGACCCCGACAGTCGA
GGAGCCCAAAACATCTGGCATCCCGAAGAAGAATCTCTTCACATACTCCCCCAGCACTAAGCGCTGGAGGCCTGACGATG
GCAGTGAAGTCACTCCATATGCCTTATCCCCTATCAGCAGCAAAAGCCAGAGTCTACTTGTATCACAACAGAAACCTACT
AAGAAGATCCCTCAAGTGCCATTCAAAGTCCTCGAGGCCTCAGGACTCCGAGATGACTTTTACTTGAACCTGTTGGATTG
GTCTTCCCTCAACATCGTCGCTGTTGGATTGAGCACTTGTGTTTATCTGTGGAGTGCTTGTACATCCCAGGTGACCAGGC
TCTTCGACCTGTGTGCTGAAGGAGATTCTGTAACCTCTGTGGGCTGGTATGAAAAAGGGAACCTGTTAGCAGTGGGCACC
CAGAAAGGCCTGGTGCAGATCTGGGATGTAGATGCTGAGAAGAAAGTGTCCACCATGGAGGGTCACAAAGCTAGAGTTGG
TGCACTGGCCTGGTACGCAGACCAGATCTCTTCTGGGAGCAGAGATACGAGGATCCTCCAGAGAGATATCCGGGCATCAC
CGCTGCAGTCTCAGCGCTGGCTGCAAGGCCACAAGCAGGAGGTGTGTGGGCTGAAGTGGTCCACAGATCACCAGCTGCTG
GCCTCAGGTGGCAACGACAACAAGCTCCTGGTCTGGAACAACTCCAATTTCAGGCCTGTCCAGCAGTATGTCACTCACAA
GGCAGCCGTGAAGGCCATCGCCTGGTCTCCCCATCAGCACGGCCTCTTAGCATCCGGTGGTGGTTCAGCCGACCGCTGCA
TTCGATTCTGGAACACGCTGACGGGGCAGCCCCTCCAGCGCATTGATACTGGCTCCCAAGTGTGCAACCTGGCCTGGTCC
AGACACGACAATGAGCTAGTCAGCACCCATGGATATGCTGAAAACCAGATTGCCGTCTGGAAATACCCCTCCCTGGTGCA
AGTGGCCAAACTCACGGGACATTTATACCGAGTCCTGTACCTGGCCGTGTCTCCTGATGGACAGGCCATAGTGACCGGGG
CCGGAGACAAGAGCCTGAGGTTCTGGAATGTTTTCCGGAAAGCCCGTTCCCAGAAGGAGTCTGCATCCGTCCTCAGTCTC
TTCACTAGAATCCGGTAA

Alignment

ORF - retro_mdom_235 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.19 %
• Parental protein coverage: 75.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKSLFTYSLSTKRSSPDDGNEVSPYSLSPVSNKSQKLLRSPRKPTRKISKIPFKVLDAPELQDDFYLNLV
          KK.LFTYS.STKR..PDDG.EV.PY.LSP.S.KSQ.LL.S..KPT.KI...PFKVL.A..L.DDFYLNL.
Retrocopy KKNLFTYSPSTKRWRPDDGSEVTPYALSPISSKSQSLLVSQQKPTKKIPQVPFKVLEASGLRDDFYLNLL

Parental  DWSSLNVLSVGLGTCVYLWSACTSQVTRLCDLSVEGDSVTSVGWSERGNLVAVGTHKGFVQIWDAAAGKK
          DWSSLN...VGL.TCVYLWSACTSQVTRL.DL..EGDSVTSVGW.E.GNL.AVGT.KG.VQIWD..A.KK
Retrocopy DWSSLNIVAVGLSTCVYLWSACTSQVTRLFDLCAEGDSVTSVGWYEKGNLLAVGTQKGLVQIWDVDAEKK

Parental  LSMLEGHTARVGALAWNADQLSSGSRDRMILQRDIRTPPVQTERRLQGHRQEVCGLKWSTDHQLLASGGN
          .S..EGH.ARVGALAW.ADQ.SSGSRD..ILQRDIR..P.Q..R.LQGH.QEVCGLKWSTDHQLLASGGN
Retrocopy VSTMEGHKARVGALAWYADQISSGSRDTRILQRDIRASPLQSQRWLQGHKQEVCGLKWSTDHQLLASGGN

Parental  DNKLLVWNHSSLSPVQQYTEHLAAVKAIAWSPHQHGLLASGGGTADRCIRFWNTLTGQPLQCIDTGSQVC
          DNKLLVWN.S...PVQQY..H.AAVKAIAWSPHQHGLLASGGG.ADRCIRFWNTLTGQPLQ.IDTGSQVC
Retrocopy DNKLLVWNNSNFRPVQQYVTHKAAVKAIAWSPHQHGLLASGGGSADRCIRFWNTLTGQPLQRIDTGSQVC

Parental  NLAWSKHANELVSTHGYSQNQILVWKYPSLTQVAKLTGHSYRVLYLAMSPDGEAIVTGAGDETLRFWNVF
          NLAWS.H.NELVSTHGY..NQI.VWKYPSL.QVAKLTGH.YRVLYLA.SPDG.AIVTGAGD..LRFWNVF
Retrocopy NLAWSRHDNELVSTHGYAENQIAVWKYPSLVQVAKLTGHLYRVLYLAVSPDGQAIVTGAGDKSLRFWNVF

Parental  SKTRSTKESVSVLNLFTRIR
          .K.RS.KES.SVL.LFTRIR
Retrocopy RKARSQKESASVLSLFTRIR

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_235 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_235 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000006919	4 retrocopies	retro_mdom_235 , retro_mdom_270, retro_mdom_296, retro_mdom_46,