RetrogeneDB ID: retro_shar_343

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841397.1:2230266..2230692(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS1
• Ensembl ID: ENSSHAG00000017422
• Aliases: None
• Description: GINS complex subunit 1 (Psf1 homolog) [Source:HGNC Symbol;Acc:28980]

Sequence

>retro_shar_343
GAGAACCACAGAGATAGACAAAGTAACTTGATTCTGACAATCAAACGCTGGCACCATTCTTTGCTGAGAAATCAAAGCTA
CATTGTTGGAGTATTTATGTGACCAATTACTCTGGATTCCAGTTCTCAGGTGGGAATGCAGCAGTGTCTTGGCAAATGCT
CTGTAATTCTGCACATCAACTGAAGAAAGGGAATAGTTCAATCATTATAAAAAGTCTCTTGCTACTTACATGAGATGTTT
GGGTAGAGATAAAGGATTAGGCCGTATACAGGCCATGAAATCCCCTAAAAGCTTATATATTGAAGTGTGATGTCTAAAAG
ACTGTGGAGAATTTGAAATTGATGATGTCCGTTCAGTTTTATTGGGGGAAAAAGTCAGTATTTTTTACCTAGATAGAAGT
ATGAACAGTTAATCATGCAAGACATC

Alignment

ORF - retro_shar_343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 58.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETKSDGRSDLIPTIKFRHSSLLRNRRCIVA-YLYDRLLRIRALRWEYGSVIPNALRFHMSAEEVEWFNHY
          E...D..S.LI.TIK..H.SLLRN...IV..YL.D.LL.I..LRWE..SV..NAL.F..S.EE.E.FNHY
Retrocopy ENHRDRQSNLILTIKRWHHSLLRNQSYIVG>YLCDQLLWIPVLRWECSSVLANAL*FCTSTEERE*FNHY

Parental  KKSLATYMRCLGGDEGLDITQDMKPPKSLYIEVRCLKDYGEFEVDDGTSVLLKK-NSQHFLPRWKCEQLI
          KKSLATYMRCLG.D.GL...Q.MK.PKSLYIEV.CLKD.GEFE.DD..SVLL....SQ.FLPR.K.EQLI
Retrocopy KKSLATYMRCLGRDKGLGRIQAMKSPKSLYIEV*CLKDCGEFEIDDVRSVLLGE<KSQYFLPR*KYEQLI

Parental  RQGV
          .Q..
Retrocopy MQDI

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_343 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002718	1 retrocopy	retro_etel_1594,
Macropus eugenii	ENSMEUG00000016481	1 retrocopy	retro_meug_1309,
Monodelphis domestica	ENSMODG00000006443	1 retrocopy	retro_mdom_1191,
Rattus norvegicus	ENSRNOG00000008091	1 retrocopy	retro_rnor_2888,
Sarcophilus harrisii	ENSSHAG00000017422	1 retrocopy	retro_shar_343 ,
Sus scrofa	ENSSSCG00000024720	1 retrocopy	retro_sscr_238,