RetrogeneDB ID: retro_mdom_1110

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:133874937..133875674(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008300
• Aliases: None
• Description: None

Sequence

>retro_mdom_1110
ATGATTCTATAGTGGATGACAGTTACTATGTTCCTTTATGCTGAAGTCTTTGCTGTGCTGTTGATCTGTATTCCTTTGAT
TTCTCCTAAAAGATGACAAAAGATCTTTAAGTCTCACCCAGTGCAGCTCAAGATAAGCTATGGTAACACCTTCTTTGCAG
TTTGGTTCTCATTGTTATTCTAGCTCTGCTTCTCATTGATGTCCTGTTGACAATATGAATGTATGATGATGTGAAGGTCA
AGAAGAACCTGCAAAATAACCCTGGGGCCATGGAGCACTTCCATATGAAGTTGTTCCAGGCCAAGAGAAATAGTGACATT
GCTGGCTTCTCTCTGCTGCTGTCATTCCTGTTAAAATACCTAGTGATCCTTATTTCCCAGTAGGTCACACTGCTGGCCTC
CAATGAGGCATTTATAAAACATGCTGAGGAGGCCAGTGAAGTCACCAAGAAATACAAGGAAGAGAATGACAAGTTGAAGA
AAAAAAAAACTGGCACTATGGCTGGCAAATTGAACCTGAAAGATGAAGTGTTGGTGGAGAACAAAAACTTGAAGGCTAAG
TTCAAGAAGCTGACTCAGGATCTGGCTGTAAGCAAGTGAAACCTGGAGAAAGCAGAAAATGAGACTTTGGCCATACATAA
GCAGTCATATGGGCTGACCAAAGAGTATGAATATCTGCTGGAGGAGCATTCATGCCTCCAGACTGCCATGGATGATCCTA
AAAACAAGAAAGCAGAG

Alignment

ORF - retro_mdom_1110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLQWTAVATFLYAEVFAVLLLCIPFISPKRWQKIFKSRLVQLVVSYGNTFFVV-LIVI--LVLLLIDAV
          M.L.W..V..FLYAEVFAVLL.CIP.ISPKR.QKIFKS..VQL..SYGNTFF.V.L..I..L.LLLID..
Retrocopy MIL*WMTVTMFLYAEVFAVLLICIPLISPKR*QKIFKSHPVQLKISYGNTFFAV<LVLIVILALLLIDVL

Parental  REIRKYDDVTEKVNLQNNPGAMEHFHMKLFRAQRNLHIAGFSLLLSFLLRRLVTLISQQATLLASNEAFK
          ..I..YDDV..K.NLQNNPGAMEHFHMKLF.A.RN..IAGFSLLLSFLL..LV.LISQ..TLLASNEAF.
Retrocopy LTI*MYDDVKVKKNLQNNPGAMEHFHMKLFQAKRNSDIAGFSLLLSFLLKYLVILISQ*VTLLASNEAFI

Parental  KQAEGASEAAKKYIEENDKLK-KGAGTGVGKLDLKDEVLAENKNLKAELKKLTQELAVNKRSLEKAENEA
          K.AE.ASE..KKY.EENDKLK....GT..GKL.LKDEVL.ENKNLKA..KKLTQ.LAV.K..LEKAENE.
Retrocopy KHAEEASEVTKKYKEENDKLKXXXXGTMAGKLNLKDEVLVENKNLKAKFKKLTQDLAVSK*NLEKAENET

Parental  LAMRKQSDGLTKEYDRLLEEHARLQVCEEGTADPREE
          LA..KQS.GLTKEY..LLEEH..LQ...........E
Retrocopy LAIHKQSYGLTKEYEYLLEEHSCLQTAMDDPKNKKAE

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_1110 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1110 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019245	1 retrocopy	retro_cfam_482,
Callithrix jacchus	ENSCJAG00000011348	1 retrocopy	retro_cjac_2552,
Echinops telfairi	ENSETEG00000008662	1 retrocopy	retro_etel_1522,
Macropus eugenii	ENSMEUG00000007345	3 retrocopies	retro_meug_1017, retro_meug_1867, retro_meug_208,
Monodelphis domestica	ENSMODG00000008300	2 retrocopies	retro_mdom_1110 , retro_mdom_24,
Sarcophilus harrisii	ENSSHAG00000009111	1 retrocopy	retro_shar_31,