RetrogeneDB ID: retro_mdom_346

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:237103847..237104274(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BIN3
• Ensembl ID: ENSMODG00000009297
• Aliases: None
• Description: bridging integrator 3 [Source:HGNC Symbol;Acc:1054]

Sequence

>retro_mdom_346
GAAAAGTTTGACAATGTTTTCCATAGTCTTAAAATGGTATTAAAGAGGTGGGAACAGGCTCTGTAGGACTCACAAGTCAT
TGCAGTCCAAAGTGGAAAAATATAAAGAAAAGGAAAAGACGAGACTGTTCCTGACCAAACTCCACCAGGTAGAAGAAGAG
TTTTGTATTGTGAGGGATGACTTTTCCATCAAGAAAAGATAACACTTGGAGGTGATGCCTCCATTCGGTATTAGCCATCT
TAACTATTTCCAGCCAAATTTTGAGTCACTGATCCAGGTCCAAGGTTGTGTACAAAACTGAGATCCACAATACTTTCAGA
GACTTAACCCAACATCTCAACCAATCTGGTCATATAGATGAGCACAGAGGGAAAGTGAATGAGCCAAGATCAATGAGCTG
CAAGCCCTATCCACAGTGGCTAATGAT

Alignment

ORF - retro_mdom_346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.38 %
• Parental protein coverage: 56.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKFGSVFPSLNMAVKRREQALQD-YKRLQSKVEKYEEKEKTGPVLAKLHQVREELRPVKDDFEAKNRQLL
          .KF..VF.SL.M..KR.EQAL.D..K.LQSKVEKY.EKEKT...L.KLHQV.EE...V.DDF..K.R..L
Retrocopy EKFDNVFHSLKMVLKRWEQAL*D>HKSLQSKVEKYKEKEKTRLFLTKLHQVEEEFCIVRDDFSIKKR*HL

Parental  EEMPRFYNSRLDYFQPSFESLI-RAQVVYYTEMHKIFRDLTQQLDQPGHTDEQREQENE-TKLSELRALS
          E.MP.F..S.L.YFQP.FESLI.R..VVY.TE.H..FRDLTQ.L.Q.GH.DE.R...NE..K..EL.ALS
Retrocopy EVMPPFGISHLNYFQPNFESLI>RSKVVYKTEIHNTFRDLTQHLNQSGHIDEHRGKVNE<AKINELQALS

Parental  IVADD
          .VA.D
Retrocopy TVAND

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	22.17 RPM
SRP007412_cerebellum	0.00 RPM	25.14 RPM
SRP007412_heart	0.00 RPM	13.76 RPM
SRP007412_kidney	0.00 RPM	68.48 RPM
SRP007412_liver	0.00 RPM	85.09 RPM
SRP007412_testis	0.00 RPM	145.95 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_346 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_346 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005470	1 retrocopy	retro_btau_1291,
Macropus eugenii	ENSMEUG00000002173	1 retrocopy	retro_meug_545,
Myotis lucifugus	ENSMLUG00000005585	1 retrocopy	retro_mluc_1238,
Monodelphis domestica	ENSMODG00000009297	1 retrocopy	retro_mdom_346 ,
Pteropus vampyrus	ENSPVAG00000006191	1 retrocopy	retro_pvam_1028,