RetrogeneDB ID: retro_mdom_899

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:364981460..364981994(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYF2
• Ensembl ID: ENSMODG00000013951
• Aliases: None
• Description: SYF2 homolog, RNA splicing factor (S. cerevisiae) [Source:HGNC Symbol;Acc:19824]

Sequence

>retro_mdom_899
GTGTGGGCTGCCCAGAAGTAGGAGGAGACATTGAGGAAGTTCTAGGAGATGCATCTGAAAAAGAGCGAAGCCCCAAAAGC
TCCATCAAGAGGTTGCGGAGAAAGATAAAAGACTTAAGCTGCCTGTAAACTAGGAAGCTAAAGCTCTTTGGAATGGGAAT
CGAAAGTTGAAGAAAAGAAAAAGGAGTGTGCTAGAAGGGGGGAAGACTATGAATGAGTGAAGCTCCTGGAGATTAGTGCT
GAGGATACAGAAAGATGGAAAAGGAAAAAGAGGAAGAACTCAGGTCTGGGCTTTTCAGACTATGCAGCTGTGCAGTTATA
CCAGTATCATTGGTTGACCAAGCAGATCAAACCTGATAAGGAAACATAAAAATTGATAGAAAAACATGAAGAAGAGTTCT
ACCCAACATCCAATAGTCTTTTTAATGGAACATATATGCCTTCTACAGAGGAAATTGATAGGCTGGTTATAGATCTAGAA
AAACAAATTGAAAAATGAGAAAAATACAGTCAGAGATATCCTTATAATTATGAC

Alignment

ORF - retro_mdom_899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 80.35 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLAAQKREERLRKFRELHLKRNEA-RKLNHQEVVEEDKRLKLPANWEAKKA-RLEWELQVEEKKKECAAR
          V.AAQK.EE.LRKF.E.HLK..EA..KL.HQEV.E.DKRLKLP.N.EA.KA..LEWE..VEEKKKECA.R
Retrocopy VWAAQK*EETLRKF*EMHLKKSEA>QKL-HQEVAEKDKRLKLPVN*EA-KA<SLEWESKVEEKKKECARR

Parental  GEDYERVKLLEISAEDAERWERKKKRKNPDLGFSDYAAAQLSQYHRLTKQIKPDMERMPLSPQEEALGEE
          GEDYE.VKLLEISAED.ERW.R.KKRKN..LGFSDYAA.QL.QYH.LTKQIKPD.E...L....E...EE
Retrocopy GEDYE*VKLLEISAEDTERWKR-KKRKNSGLGFSDYAAVQLYQYHWLTKQIKPDKET*KLIEKHE---EE

Parental  FYPTSNSLLHGTHVPSTEEVDRMVIDLEKHVSKDKKYSRRRPYNDD
          FYPTSNSL..GT..PSTEE.DR.VIDLEK...K..KYS.R.PYN.D
Retrocopy FYPTSNSLFNGTYMPSTEEIDRLVIDLEKQIEK*EKYSQRYPYNYD

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_899 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_899 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010115	1 retrocopy	retro_amel_566,
Bos taurus	ENSBTAG00000001651	1 retrocopy	retro_btau_478,
Choloepus hoffmanni	ENSCHOG00000005273	1 retrocopy	retro_chof_2034,
Callithrix jacchus	ENSCJAG00000018559	1 retrocopy	retro_cjac_467,
Homo sapiens	ENSG00000117614	1 retrocopy	retro_hsap_4152,
Monodelphis domestica	ENSMODG00000013951	1 retrocopy	retro_mdom_899 ,
Oryctolagus cuniculus	ENSOCUG00000013050	1 retrocopy	retro_ocun_1522,
Sarcophilus harrisii	ENSSHAG00000007152	1 retrocopy	retro_shar_15,