RetrogeneDB ID: retro_shar_464

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849588.1:1741090..1741880(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCD2
• Ensembl ID: ENSSHAG00000013118
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 [Source:HGNC Symbol;Acc:11107]

Sequence

>retro_shar_464
AATCCCAGCAAACAAAGAAGGAGTTTTCTTCATTTTTTAAGAGTCTAGACAAGGAGCTTTATGGACCTGATAACCATCTG
TAGACTGGCACTCTTTGCCTACAACCCAAGAGACAGATGGCTTCCAAGTGAAACTCCCTGGGGACTTTAATGTCAAGTGT
ATTTTCCTGCCTATGCTGGATCATCAGCCACCCCAGTATAAGCTGGACCCCCAGTTGGCTCGGCTACTTGGTGAGCCCAC
CCAGACCCAGGCTGCCATCATGCAGGCACTGTGGTTGTACATTAAGCACAACCCTTTGCAAGATGGGCACGAGCATGAAT
ACATCCACTCCAACCACTACTTTCCTCAGATCTATAGATGCGGGCATCTTTGTTTCTCTGAGATACCCATGAAACTGGCT
GGGCTATTGTAGCATCCAGACCCCATTGTCATCAATCATGTCATCAGTGTGGACCCCAATGACCAAAAGAACATGGCATG
ATATTGATATTGATGTTGAAGTGGATGATCCACTCAAGGCACAGATGAGCAACTTTCTAGCCTCCACCACCAACCAACAG
GAGATTGCATCCCTGGATGCTGAGATTTATGAAACCATTGAGTCCATCAACCAGTTGAAAACTCAGAAGGATTTCATGCT
CTGTTTCAGCACTGACCCACAGGACTTCATTCAGGAATGGCTATGTTCTCAGCAAGGAGATCTCAAGATCATCACAGACA
TGATAGTAACCCAAAGGAAGAAAGGCGAGCTGCTTTCTACCATCAGCCCTGAGCTTAGGAAGTTAGAGGC

Alignment

ORF - retro_shar_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.62 %
• Parental protein coverage: 50.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DPSKQKR-KFSSFFKSLVIELDKELYGPDNHL-VEWHRLPTTQETDGFQVKRPGDLNVKCTLLLMLDHQP
          .PSKQ.R..FSSFFKS....LDKELYGPDNHL.V.WH.LPTTQETDGFQVK.PGD.NVKC..L.MLDHQP
Retrocopy NPSKQRR<EFSSFFKS----LDKELYGPDNHL<VDWHSLPTTQETDGFQVKLPGDFNVKCIFLPMLDHQP

Parental  PQYKLDPRLARLLGVHTQTRAAIMQALWLYIKHNQLQDGHEHEYINCNRYFRQIFSCGRLRFSEIPMKLA
          PQYKLDP.LARLLG..TQT.AAIMQALWLYIKHN.LQDGHEHEYI..N.YF.QI..CG.L.FSEIPMKLA
Retrocopy PQYKLDPQLARLLGEPTQTQAAIMQALWLYIKHNPLQDGHEHEYIHSNHYFPQIYRCGHLCFSEIPMKLA

Parental  GLLQHPDPIVINHVISVDPNDQKKTACY-DIDVEVDDPLKAQMSNFLASTTNQQEIASLDVKIHETIESI
          GLL.HPDPIVINHVISVDPNDQK..A.Y.DIDVEVDDPLKAQMSNFLASTTNQQEIASLD..I.ETIESI
Retrocopy GLL*HPDPIVINHVISVDPNDQKNMA*Y>DIDVEVDDPLKAQMSNFLASTTNQQEIASLDAEIYETIESI

Parental  NQLKTQRDFMLSFSTDPQDFIQEWLRSQRRDLKIITDVI-GNPEEERRAAFYHQPWAQEAVG
          NQLKTQ.DFML.FSTDPQDFIQEWL.SQ..DLKIITD.I..NP.EERRAAFYHQP.A.E..G
Retrocopy NQLKTQKDFMLCFSTDPQDFIQEWLCSQQGDLKIITDMI<SNPKEERRAAFYHQP*A*EVRG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_464 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012708	1 retrocopy	retro_cfam_256,
Callithrix jacchus	ENSCJAG00000019528	1 retrocopy	retro_cjac_2323,
Mustela putorius furo	ENSMPUG00000014835	1 retrocopy	retro_mputfur_89,
Sarcophilus harrisii	ENSSHAG00000013118	1 retrocopy	retro_shar_464 ,
Tursiops truncatus	ENSTTRG00000006988	1 retrocopy	retro_ttru_1394,