RetrogeneDB ID: retro_mdom_594

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:438937959..438938513(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000009896
• Aliases: None
• Description: None

Sequence

>retro_mdom_594
ATAAGAAAGTGCTTTTTTTCACCTGCCAAGACCAGATTCACAACTGGCATCTCATATACCACTGTTATTCAGAATATGAA
CAAACTGAAGTGACTATCAGAGGAAAGAAAGATATTGTAGCAGGTGTCATCTTACCAATGTTTGGACATTATCAAGAAGG
AGTTGACAGTCATAAATTGATTGGTTTGACCATAGGTGGGGAACAACTGTCTCAACTGAGGAGGAATAATACCAAAGTAT
AGGAGCTATTGGTGAAACTGGTATTACTGCGCACGTCATTTGTTACACTGGATGAGGCCATTAAAATAACAAACAGATGG
ATGAATGCCATTGAGCATGTGATCATTCCCTGGATTCAGTGTACATTTGCTTTCATCATCAAAGAATTGGATGAATGAGA
GCATGGAGAGTTTGACAGGTTAAAGAAAATATGGGAGAAAAAAGGGTTCTCATAGAGAAAACAGAGGGAATTGGAGCTCC
AGAAGGTAACTGGAGAAGTGTAGGAGCCTGCTAATCTGCTGGCTGAAGAGAAGAATGAAGGTCTTCTGTTTAAA

Alignment

ORF - retro_mdom_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.22 %
• Parental protein coverage: 81.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MREAAFSLAEAKFTAGDFSATVIQNVNK-AQVKIRTKKDNVAGVTLPVFEHYHEGTDSYELTGLARGGEQ
          .R...FS.A...FT.G....TVIQN.NK...V.IR.KKD.VAGV.LP.F.HY.EG.DS..L.GL..GGEQ
Retrocopy IRKCFFSPAKTRFTTGISYTTVIQNMNK<TEVTIRGKKDIVAGVILPMFGHYQEGVDSHKLIGLTIGGEQ

Parental  VTKLKKNYGKAVELLVELASLQTSFITLDEAIKITNRRVNAIEHVIIPRIERTLNYIVTELDEREREEFY
          ...L..N..K..ELLV.L..L.TSF.TLDEAIKITNR..NAIEHVIIP.I..T...I..ELDE.E..EF.
Retrocopy LSQLRRNNTKV*ELLVKLVLLRTSFVTLDEAIKITNRWMNAIEHVIIPWIQCTFAFIIKELDE*EHGEFD

Parental  RLKKIQEKKKSVKEKLEKEISCLKASGELPEPANLLAIEKDEDLLFE
          RLKKI.E.KK........E....K..GE..EPANLLA.EK.E.LLF.
Retrocopy RLKKIWE-KKGFS*RKQRELELQKVTGEV*EPANLLAEEKNEGLLFK

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	139.70 RPM
SRP007412_cerebellum	0.00 RPM	157.35 RPM
SRP007412_heart	0.00 RPM	78.94 RPM
SRP007412_kidney	0.00 RPM	123.78 RPM
SRP007412_liver	0.00 RPM	76.03 RPM
SRP007412_testis	0.00 RPM	623.68 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_594 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_594 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 15 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008240	1 retrocopy	retro_amel_332,
Bos taurus	ENSBTAG00000016309	2 retrocopies	retro_btau_1757, retro_btau_408,
Canis familiaris	ENSCAFG00000016369	2 retrocopies	retro_cfam_1186, retro_cfam_999,
Choloepus hoffmanni	ENSCHOG00000003733	5 retrocopies	retro_chof_1229, retro_chof_2711, retro_chof_54, retro_chof_926, retro_chof_938,
Cavia porcellus	ENSCPOG00000009085	1 retrocopy	retro_cpor_36,
Felis catus	ENSFCAG00000011078	1 retrocopy	retro_fcat_632,
Myotis lucifugus	ENSMLUG00000006244	5 retrocopies	retro_mluc_2345, retro_mluc_442, retro_mluc_540, retro_mluc_666, retro_mluc_94,
Macaca mulatta	ENSMMUG00000021418	1 retrocopy	retro_mmul_1159,
Monodelphis domestica	ENSMODG00000009896	5 retrocopies	retro_mdom_1196, retro_mdom_1522, retro_mdom_1730, retro_mdom_390, retro_mdom_594 ,
Mustela putorius furo	ENSMPUG00000007002	2 retrocopies	retro_mputfur_1381, retro_mputfur_748,
Otolemur garnettii	ENSOGAG00000015052	1 retrocopy	retro_ogar_966,
Sus scrofa	ENSSSCG00000002288	1 retrocopy	retro_sscr_357,
Ictidomys tridecemlineatus	ENSSTOG00000027710	1 retrocopy	retro_itri_383,
Vicugna pacos	ENSVPAG00000005696	1 retrocopy	retro_vpac_232,
Drosophila melanogaster	FBgn0040377	1 retrocopy	retro_dmel_70,