RetrogeneDB ID: retro_mdom_270

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:26530354..26531764(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025321
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_mdom_270
ATGAGCTGGAGCCTGGCGCTGCCGCCCACTGCTCCGGTGCCCTCTGCCAGCAAATACGGAGACCGCTACATTCCCTCTCG
GGTGGCCGCCAACTGGGAAGTGCACTTCCACAGCAAAGATGAGTCTGAGTTATCTTCTGGGCCAAAGCAGAAAACAGAAG
ACTCCAACTCTGGCAAGAACAGAAGTAGTCTCGTCTACTCCACCGCGTTGAAGAACGAGCTGCTGGGAGCTCGGATACAG
AAGGCCCCAAGCCTGGAGTCAGAGGAGAACCAAAGCCCACAGCCTTGTGGACCAACCAAAAGGAATCTTTTCACCTACTC
TCCTAACACCTTCCGCTGGAGACCCGAGATAGGCAGTGAGATGTCAGCCTATGCTATGTCACCCATCAGCAAGAGCAGTC
AGACCTTACTAACCACTGTGCAGAGAGAGGCCAGAATCATTCCCAAAAGCCCCTTCAGAATCCTCGAGGCTCCTGAACTC
AGTGACGACTTCTACTTGAACCTGCTGGATTGGTCTCGCCACAACATTGTTGCCGTGGGCCTGGGCAGTACTGTTTTCCT
GTGGAGTGCCACTACCAGCCAGGTCACGGAACTGTGTGACCTCGCTCAGGAAGATGATGCTGTGACCTCTGTGAGTTGGA
CTGAACGTGGGACCTTGTTAGCTGTTGGCACACAGAAAGGTGTTGTGCAGATCTGGGATGCAGATGCGGAGAAGAGAGTG
GCCACAATGGAGGGCCACTCGGGCAGGGTCAGCTCATTGGCCTGGAATGGGAGCCAGATTTCTTCTGGGAGCAGAGACCG
AAGGATCAACCAGAGAGATATCCGGGCTTACCCCCTGCAGTCTCAGCGCTGGCTGCAAGGCCACAAGCAGGAGGTGTGTG
GGCTGAAGTGGTCCACAGATCACCGGCTGCTGGCCTCAGGTGGCAACGACAACAGGCTGCTGCTCTGGAATTGCTACAGT
TTAAAGCCCGTCCAGAAGTACACTGCTCACAAGGCAGCTGTGAAGGCCATCGCCTGGTCTCCCCATCAGCACCGCCTCTT
AGCATCCGGTGGTGGTTCAGCCGACCGCTGCATTCGATTCTGGAACACGCTGACGGGGCAGCCCCTCCAGCATGTCGATA
CTGGCTCCCAAGTGTGCAACCTGGCCTGGTCCAAGCAGGACAATGAGCTAGTCAGCACCCATGGTTACTCAGAAAACCAG
ATCGTCATCTGGAAATACCCATCTATGACCCAAGTGGCCAAACTCACGGGACATTTATACCGAGTCCTGTACCTGGCCGT
GTCTCCTGATGGACAGACCATAGTGACCGGGGCCGGAGACAAGAGCCTGAGGTTCTGGAATGTTTTCCGGAAAGCCTGTG
CCCAGAAGGAGTCTGCATCTGTCCTCAGTCTCTTCACTAGAATCCGGTAA

Alignment

ORF - retro_mdom_270 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.37 %
• Parental protein coverage: 93.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSNSPMSSPSKHGDRFIPSRAGANWSINFHRINENEKSPSQNRKAKDATSDNGKDGLAYSALLKNELLGA
          P...P..S.SK.GDR.IPSR..ANW...FH...E.E.S.....K..D..S......L.YS..LKNELLGA
Retrocopy PPTAPVPSASKYGDRYIPSRVAANWEVHFHSKDESELSSGPKQKTEDSNSGKNRSSLVYSTALKNELLGA

Parental  GIEKVQDPQTEDRRL-QPSTPEKKSLFTYSLSTKRSSPDDGNEVSPYSLSPVSNKSQKLLRSPRKPTRKI
          .I.K......E.....QP..P.K..LFTYS..T.R..P..G.E.S.Y..SP.S..SQ.LL.......R.I
Retrocopy RIQKAPSLESEENQSPQPCGPTKRNLFTYSPNTFRWRPEIGSEMSAYAMSPISKSSQTLLTTVQREARII

Parental  SKIPFKVLDAPELQDDFYLNLVDWSSLNVLSVGLGTCVYLWSACTSQVTRLCDLSVEGDSVTSVGWSERG
          .K.PF..L.APEL.DDFYLNL.DWS..N...VGLG..V.LWSA.TSQVT.LCDL..E.D.VTSV.W.ERG
Retrocopy PKSPFRILEAPELSDDFYLNLLDWSRHNIVAVGLGSTVFLWSATTSQVTELCDLAQEDDAVTSVSWTERG

Parental  NLVAVGTHKGFVQIWDAAAGKKLSMLEGHTARVGALAWNADQLSSGSRDRMILQRDIRTPPVQTERRLQG
          .L.AVGT.KG.VQIWDA.A.K.....EGH..RV..LAWN..Q.SSGSRDR.I.QRDIR..P.Q..R.LQG
Retrocopy TLLAVGTQKGVVQIWDADAEKRVATMEGHSGRVSSLAWNGSQISSGSRDRRINQRDIRAYPLQSQRWLQG

Parental  HRQEVCGLKWSTDHQLLASGGNDNKLLVWNHSSLSPVQQYTEHLAAVKAIAWSPHQHGLLASGGGTADRC
          H.QEVCGLKWSTDH.LLASGGNDN.LL.WN..SL.PVQ.YT.H.AAVKAIAWSPHQH.LLASGGG.ADRC
Retrocopy HKQEVCGLKWSTDHRLLASGGNDNRLLLWNCYSLKPVQKYTAHKAAVKAIAWSPHQHRLLASGGGSADRC

Parental  IRFWNTLTGQPLQCIDTGSQVCNLAWSKHANELVSTHGYSQNQILVWKYPSLTQVAKLTGHSYRVLYLAM
          IRFWNTLTGQPLQ..DTGSQVCNLAWSK..NELVSTHGYS.NQI..WKYPS.TQVAKLTGH.YRVLYLA.
Retrocopy IRFWNTLTGQPLQHVDTGSQVCNLAWSKQDNELVSTHGYSENQIVIWKYPSMTQVAKLTGHLYRVLYLAV

Parental  SPDGEAIVTGAGDETLRFWNVFSKTRSTKESVSVLNLFTRIR
          SPDG..IVTGAGD..LRFWNVF.K....KES.SVL.LFTRIR
Retrocopy SPDGQTIVTGAGDKSLRFWNVFRKACAQKESASVLSLFTRIR

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_270 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_270 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,