RetrogeneDB ID: retro_shar_132

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834426.1:600543..600891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PBDC1
• Ensembl ID: ENSSHAG00000017872
• Aliases: None
• Description: polysaccharide biosynthesis domain containing 1 [Source:HGNC Symbol;Acc:28790]

Sequence

>retro_shar_132
TCAGATGACCCTCTGTTTCTAAAACTCACTAAAGTAGGTGACCAGATCTAGTCGGAGTCCCAGGAGAATTTAGAAAGCGC
AAGATAGCTGTGTTGGACCTAGAAGAACTCAGATCAGAACCATGGAGACCATTTGATATGAAGTTCAATGGTATTGTTGA
AGATTTCAACTCCTGCATGCTGCTACAGCTAGACTGTTCTCAGGAGTATAGTAAAGAAAACACCACCTTGCTATTAAGGA
CACAGTTTTTAGCTATTGAAATAGCCTGGAACCAGGAAGGTTCTAACCGAGCTGTTATAACAGTGCTCACAGAACAGAGA
CCCAGAGAAAGACAATGCGATGTCTAGG

Alignment

ORF - retro_shar_132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.71 %
• Parental protein coverage: 71.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVDPLFLRLTKVDDQIYSEFRES-FGKLKIDVLDPEELKSEPAKEKWRPFCMKFNGIVEDFNYGTLLRLD
          S.DPLFL.LTKV.DQI.SE..E..F.K.KI.VLD.EEL.SEP....WRPF.MKFNGIVEDFN...LL.LD
Retrocopy SDDPLFLKLTKVGDQI*SESQEN<FRKRKIAVLDLEELRSEP----WRPFDMKFNGIVEDFNSCMLLQLD

Parental  CTQGYSEENTIFATRIQFFAIEIARNREGYNRAV-YNGG-QQNGASEKDSTMPR
          C.Q.YS.ENT....R.QF.AIEIA.N.EG.NRAV.YN....QN...EKD..M.R
Retrocopy CSQEYSKENTTLLLRTQFLAIEIAWNQEGSNRAV<YNSA<SQNRDPEKDNAMSR

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_132 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132 ,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979,