RetrogeneDB ID: retro_mdom_934

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:491148976..491149476(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF5
• Ensembl ID: ENSMODG00000011362
• Aliases: None
• Description: serine/arginine-rich splicing factor 5 [Source:HGNC Symbol;Acc:10787]

Sequence

>retro_mdom_934
ATAAGTAGCTATAGAATATTTATTGGAAGGTTAAATCTGGCAGCTCAAGAAAAAAGATGTAGAAAGATTCTTTAAATGTT
ATGGACTAATCAGAAACATTGATCTAGAGAGAGGCTTTGGGTTTGTGAAATCTGAAGACTCAAGAGATGCTGATGATTCT
ATCTGCAAACTTTATGGAAGGAATTCTGCAGTGAAAAGGTTACAGTTGAACATACTAGGGCTCATTCTTAAGGTGGATGA
TGAAGAGATTTATATTCTGATCATTTTAGTAGTGGTTGTTCCCAAAACCATAGGAGAAATGTACTGTCTGTGTGAACAGA
AAAATTTTCTAGAGTTGAGAATTTATCTTCATGAATTGGCTGGCAGAATCTCAAAGATTTCATAAGGCAGACTGGGGAAT
TACCCTTATCAGACACTCATAAAACTAAACTAAATGAATTGGTGGTTGAATTTGCCTCTTAGAGTCATTAAATAATGCTA
TCAATAAACTTTCTGGAAAA

Alignment

ORF - retro_mdom_934 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.94 %
• Parental protein coverage: 62.78 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGCRVFIGRLNPAAREK-DVERFFKGYGRIRDIDLKRGFGFVEFEDPRDADDAVYELDG-KELCSERVT
          .S..R.FIGRLN.AA.EK.DVERFFK.YG.IR.IDL.RGFGFV..ED.RDADD....L.G.KE.CSE.VT
Retrocopy ISSYRIFIGRLNLAAQEK>DVERFFKCYGLIRNIDLERGFGFVKSEDSRDADDSICKLYG<KEFCSEKVT

Parental  IEHARARSRGGRGRGRYSDRFSSRRPRNDRRNAPPVRTENRLIVENLSSRVSWQDLKDFMRQAGEVTFAD
          .EH.RA.S.GG..R..YSD.FSS....N.RRN...V.TE....VENLSS...WQ.LKDF.RQ.GE....D
Retrocopy VEHTRAHS*GG**RDLYSDHFSSGCSQNHRRNVLSV*TEKFSRVENLSS*IGWQNLKDFIRQTGELPLSD

Parental  AHRPKLNEGVVEFASYS-DLKNAIEKLSGK
          .H..KLNE.VVEFAS.S..L.NAI.KLSGK
Retrocopy THKTKLNELVVEFAS*S<SLNNAINKLSGK

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	662.97 RPM
SRP007412_cerebellum	0.00 RPM	788.06 RPM
SRP007412_heart	0.00 RPM	369.40 RPM
SRP007412_kidney	0.00 RPM	611.01 RPM
SRP007412_liver	0.00 RPM	443.57 RPM
SRP007412_testis	0.00 RPM	555.91 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_934 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_934 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001521	2 retrocopies	retro_meug_1173, retro_meug_2182,
Monodelphis domestica	ENSMODG00000003107	1 retrocopy	retro_mdom_697,
Monodelphis domestica	ENSMODG00000008669	1 retrocopy	retro_mdom_289,
Monodelphis domestica	ENSMODG00000011362	1 retrocopy	retro_mdom_934 ,
Mus musculus	ENSMUSG00000021134	1 retrocopy	retro_mmus_2396,
Rattus norvegicus	ENSRNOG00000005513	1 retrocopy	retro_rnor_2900,
Tupaia belangeri	ENSTBEG00000001972	1 retrocopy	retro_tbel_2707,