RetrogeneDB ID: retro_shar_150

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834472.1:1460024..1460809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R36
• Ensembl ID: ENSSHAG00000010522
• Aliases: None
• Description: protein phosphatase 1, regulatory subunit 36 [Source:HGNC Symbol;Acc:20097]

Sequence

>retro_shar_150
ATCTTGGCATTGTTATACCACTTATCTCATTATCTGGAAATACTTTCATTGAAAAAGAAACCCAAAAGCTACATGGAAAG
CCATATAGAGAAAAAGGAGATGGAATTAGTTACTATGAGATTATGAGAGTCACAGAAATATCTTGTTCAGAAATATTGCA
TTGTTGTTTTAGATTTGAGAATGTCTGATAAGCAACTCATGACCTGTGGGAAAGAAAAAGCTTCAGATACACAAAAAGAC
TGGAAGTTTTTTGAAGCTTTCTTTATGTTCTATACATATATAGCATGGATAGTATTCTGACACAAGTACATAACTGAGAC
TGATGAAATAGGTAAGCTCTTTTGTAGTCATATGTTTCAATCATGAGAGAAGAAGGCAGGAGGATGAAGAATCTGGTGAG
GAAAAGAGAAGAATGATTTTTGTGTAATTCAGGAGAATGACAGTCAAGCTGAGAGCAACAAAAACAACAATTCATATGCA
TTCTCCAGTCTTATCCACTCTTATTCCCTCCCTAAAGAACATGCTCAGCATCTTTGTGAGAACTGTGGTTGGATAAATGT
CCCCTTTCAACAATCCAACCAAAAAGAATTGGTCAGCCATGACTCAATCACCCTGTCACTAGTTGGCACCTTAGGGGAAT
CTTGAACCCTATTCAACCCTATTCTCTTCTCTCCAATAAACAAAAACAGAATCTGGAGCCTACAAAGAGAAATGCTTTCC
TCTTAACTGAAAATAATGCCAAGGTTCAAGAGACATTGGAGTCAGCCATGAAAGTGTTATCTCCA

Alignment

ORF - retro_shar_150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.04 %
• Parental protein coverage: 72.93 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LMALLYYLSHYLEKLSLEKKPKSYMASHVEKREMELVIEKLQESQKYLAQKYCSLVLGLGMPDKHHMACG
          ..ALLY.LSHYLE.LSL.KKPKSYM.SH.EK.EMELV...L.ESQKYL.QKYC..VL.L.M.DK..M.CG
Retrocopy ILALLYHLSHYLEILSLKKKPKSYMESHIEKKEMELVTMRL*ESQKYLVQKYCIVVLDLRMSDKQLMTCG

Parental  KEKISDTQKDWKFFEAFFTFCTYVAWVVFRREHLKEIDEEIGRLFRTNM-FNSARRRREDEESGDEKRTM
          KEK.SDTQKDWKFFEAFF.F.TY.AW.VF......E.D.EIG.LF...M.FN..RRR.EDEESG.EKR.M
Retrocopy KEKASDTQKDWKFFEAFFMFYTYIAWIVF*HKYITETD-EIGKLFCSHM>FNHERRRQEDEESGEEKRRM

Parental  TFVQFRKMMAKRPAIKTTIHLRSPALSTLLPS-PKEHAQHLFEKSRSRMGVPLQQSSQKELVNYDSVAMP
          .FV.FR.M..K..A.KTTIH..SP.LSTL.PS.PKEHAQHL.E.......VP.QQS.QKELV..DS....
Retrocopy IFV*FRRMTVKLRATKTTIHMHSPVLSTLIPS<PKEHAQHLCENC-GWINVPFQQSNQKELVSHDSITLS

Parental  VVGIIGEPRSLFN-PSTLLPSEEEQTPEPTKRNASLINENNAKVQEILELAMKLLGP
          .VG..GE...LFN.P..LL.....Q..EPTKRNA.L..ENNAKVQE.LE.AMK.L.P
Retrocopy LVGTLGES*TLFN<PYSLLSNKQKQNLEPTKRNAFLLTENNAKVQETLESAMKVLSP

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_150 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000010522	1 retrocopy	retro_shar_150 ,