RetrogeneDB ID: retro_mdom_259

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:429144261..429145317(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000010616
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005918
• Aliases: None
• Description: None

Sequence

>retro_mdom_259
ATGTTTTCGTTCTCGGAGCTCCACTTCAACGCAAACAACGGCTACTTGGAGGGGCTGGTCCGGGGCTTAAAGACGGGATT
GTTAACCCACTTCGATTACACGAACCTGGTGCAGTGCGAGTCGCTGGAGGATCTGAAACTCCACCTTCAGACCACAGCCT
ACGGGAACTTCCTGGCGAATGAGGTCTCCCCACTCTCCGTGTCCATGATTGACGACAGAATGAGGGAGAAGTTGGTGTCA
GAGTTCTTCTACCTGAGGAACCAGGCATTTGAACCGCTGAGCAAGTTCCTGGACTTCATCACCTACAGCTACATGATCGA
CAACGTCATCCTGCTGTTAACGGGCACCCTACACGAGCGCTCCATCTCCGAGCTCATGCCCAAGTGCCACCCTCTGGGCC
ACTTTGATCAGATAGAGGCCGTGAACATCGCTCAGACACAAGAAGAGCTGTACAACGCTATCTTGGTGGACTCTCCGCTC
GCTATCTTCTTCCAGACCCACTTTTCTAAGGAGGAACTCCAGCAGCTGAACATCGAAATCCTCCGCAACACGATGTACAA
ATCCTACCTGGAATCTTTCTATCAATTCTGCACCCTGCTGGGGGGCATCACAGCTGAGGTCATGAATCCCATCTTGGAGT
TTGAGGCGGACAGAAGGGCCTTCATCATCACCATCAACTCGTTTGGCACCGAACTCTCCAAGCAAGCCCGGGCCAATCTC
TTCCCCAATTGTGGGCTGCTCTACCCGCAGGGTCAGGCCCTTCTGGCACAGGCCAATGAGTTCAAGGAGGTCAAAGCGGT
GGCTGACTTCTACCCACAATATAAAGAGCTTTTTGAAGCAGTTAGCTCCAATGGTGGAGGTAAGACCTTGGAGGACCGAT
TCTTTGAGCATGAGGTGAACCTGAACAAACTGGCCTTTCTCAGACAGTTCCACTTTGGCATCTTCTACGCCTTCGTGAAG
CTTAAGGAGCAGGAGTGCCGGAATGTTGTGTGGATTGCTGAGTGTATCGCCCAGAACCACCGGAACAAGATCAGAAATTA
CATTGACATCTTTTAG

Alignment

ORF - retro_mdom_259 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSFPELYFNVDNGYLEGLVRGFKAGVLSQQDYLNLVQCETLEDLKLHLQSTDYGNFLANEASPLTVSVI
          M.SF.EL.FN..NGYLEGLVRG.K.G.L...DY.NLVQCE.LEDLKLHLQ.T.YGNFLANE.SPL.VS.I
Retrocopy MFSFSELHFNANNGYLEGLVRGLKTGLLTHFDYTNLVQCESLEDLKLHLQTTAYGNFLANEVSPLSVSMI

Parental  DDKLKEKMVMEFRHMRNHAYEPLASFLDFITYSYMIDNVILLITGTLHQRSIAELVPKCHPLGSFEQMEA
          DD...EK.V.EF...RN.A.EPL..FLDFITYSYMIDNVILL.TGTLH.RSI.EL.PKCHPLG.F.Q.EA
Retrocopy DDRMREKLVSEFFYLRNQAFEPLSKFLDFITYSYMIDNVILLLTGTLHERSISELMPKCHPLGHFDQIEA

Parental  VNIAQTPAELYNAILVDTPLAAFFQDCISEQDLDEMNIEIIRNTLYKAYLESFYKFCTLLGGTTADAMCP
          VNIAQT..ELYNAILVD.PLA.FFQ...S...L...NIEI.RNT.YK.YLESFY.FCTLLGG.TA..M.P
Retrocopy VNIAQTQEELYNAILVDSPLAIFFQTHFSKEELQQLNIEILRNTMYKSYLESFYQFCTLLGGITAEVMNP

Parental  ILEFEADRRAFIITINSFGTELSKEDRAKLFPHCGKLYPEGLAQLARADDYEQVKTVADYYQEYKLLFEG
          ILEFEADRRAFIITINSFGTELSK..RA.LFP.CG.LYP.G.A.LA.A.....VK.VAD.Y..YK.LFE.
Retrocopy ILEFEADRRAFIITINSFGTELSKQARANLFPNCGLLYPQGQALLAQANEFKEVKAVADFYPQYKELFEA

Parental  AGNNPGDKTLEDRFFEHEVKLNKLAFLNQFHFGVFYAFVKLKEQECRNIVWIAECIAQRHRAKIDNYIPI
          ...N.G.KTLEDRFFEHEV.LNKLAFL.QFHFG.FYAFVKLKEQECRN.VWIAECIAQ.HR.KI.NYI.I
Retrocopy VSSNGGGKTLEDRFFEHEVNLNKLAFLRQFHFGIFYAFVKLKEQECRNVVWIAECIAQNHRNKIRNYIDI

Parental  F
          F
Retrocopy F

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_259 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_259 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
Macropus eugenii	ENSMEUG00000014351	1 retrocopy	retro_meug_1680,
Monodelphis domestica	ENSMODG00000005918	2 retrocopies	retro_mdom_1270, retro_mdom_259 ,
Sarcophilus harrisii	ENSSHAG00000013154	1 retrocopy	retro_shar_102,