RetrogeneDB ID: retro_mdom_74

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:195865638..195866598(+)
• Located in intron of: ENSMODG00000010443

Retrocopy information

• Ensembl ID: ENSMODG00000010451
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005569
• Aliases: None
• Description: None

Sequence

>retro_mdom_74
TGCTCAACACAGCCCATCCAGAAGGATCAAGAACGGGTGCCCGAAGTGTTGGCGGTGGCGACCCCTCTGGCCATCTTCTA
CCATGTGCGCTACGAGAACCTGGTGGGGGGCGTGATTGGGGGTATCCTCTCCAACCTGGTGCTGCACCCCATGGACCTCG
TGAAGATCCGCTTCGCAGTGAGTGACGGCCTCAGAGTGAGGCCCAAGTACAGAGGCATCGCCCACTGTCTGCACACTATT
TGGAAACAAGACGGCGTGCGAGGCCTCTATCAAGGACTCACCCCAAACGTGTGGGGAGCCGGGTTATCCTGGGGACTCTA
CTTTTGCTTCTATAATGCCATTAAGTCGTACAAGTCAGAGGGAAGAACAGACCAGCTAAAGGCGCCTGATTATCTTTTCT
CTGCTGCTCAAGCTGGTGCTATGACACTGTGTTTCACAAACCCCTTGTGGGTGACCAAGACCCGGCTCATGTTACAGTAT
GACCACAGTCCTGAGAAGAGGAAGTATGATGGCATGATTGACACTTTGGTCAAGATCTACAAAGCTGATGGTGTGCGGGG
GCTGTACAGGGGATTTATGCCTGGGCTGCTGGGAACATCTCACGGAGCACTTCAGTTCATGACATATGAAATGTTGAAAA
AAAGGTACAATGAACACATGGCTAGAATGCAAGAGGCACAGCTGAGCACCATCGAATATATATCAATTGCAGCAATTGCA
AAAATATTTGCAGTGGCAGCCACGTACCCATATCAGGTAGTGAGAGCCCGACTTCAAGATCAGCACATCTATTATCAGGG
TATACGACATGTAATCAGAAGGACATGGAAGAAAGAAGGCATTCAAGGATTTTACAAAGGAATTGTCCCTAATTTGATTA
CAGTGACTCCAGCCTGTTGTATTACTTTTGTAGTTTATGAAAATGTCTCCCAATTTTTATGTGACTTGAGAGAAGGCCCT

Alignment

ORF - retro_mdom_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.31 %
• Parental protein coverage: 93.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVFRHVRYENLVAGVSGGVLSNLALHPLDLVKIRFAVSDGLELRPKYNGIVHCLTTIWKVDGLRGLYQGV
          A.F.HVRYENLV.GV.GG.LSNL.LHP.DLVKIRFAVSDGL..RPKY.GI.HCL.TIWK.DG.RGLYQG.
Retrocopy AIFYHVRYENLVGGVIGGILSNLVLHPMDLVKIRFAVSDGLRVRPKYRGIAHCLHTIWKQDGVRGLYQGL

Parental  TPNVWGAGLSWGLYFFFYNAIKSYKTEGRTEPLDATEYLVSAAEAGAMTLCITNPLWVTKTRLMLQYNVV
          TPNVWGAGLSWGLYF.FYNAIKSYK.EGRT..L.A..YL.SAA.AGAMTLC.TNPLWVTKTRLMLQY...
Retrocopy TPNVWGAGLSWGLYFCFYNAIKSYKSEGRTDQLKAPDYLFSAAQAGAMTLCFTNPLWVTKTRLMLQYDH-

Parental  SSSQRQYKGMIDTLVKLYKYEGVRGLYKGFLPGLFGTSHGALQFMAYELLKLKYNTHVSRLPDEQLSTIE
          S...R.Y.GMIDTLVK.YK..GVRGLY.GF.PGL.GTSHGALQFM.YE.LK..YN.H..R....QLSTIE
Retrocopy SPEKRKYDGMIDTLVKIYKADGVRGLYRGFMPGLLGTSHGALQFMTYEMLKKRYNEHMARMQEAQLSTIE

Parental  YISIAALSKIFAVAATYPYQVVRARLQDQHIFYKGVLDVIVRTWRKEGILGFYKGIVPNLIRVTPACCIT
          YISIAA..KIFAVAATYPYQVVRARLQDQHI.Y.G...VI.RTW.KEGI.GFYKGIVPNLI.VTPACCIT
Retrocopy YISIAAIAKIFAVAATYPYQVVRARLQDQHIYYQGIRHVIRRTWKKEGIQGFYKGIVPNLITVTPACCIT

Parental  FVVYENVSHFLLGLR
          FVVYENVS.FL..LR
Retrocopy FVVYENVSQFLCDLR

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_74 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_74 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
Monodelphis domestica	ENSMODG00000005569	1 retrocopy	retro_mdom_74 ,
Monodelphis domestica	ENSMODG00000013036	1 retrocopy	retro_mdom_1808,
Otolemur garnettii	ENSOGAG00000002276	2 retrocopies	retro_ogar_3038, retro_ogar_331,