RetrogeneDB ID: retro_shar_635

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856880.1:907464..907977(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF1
• Ensembl ID: ENSSHAG00000004637
• Aliases: None
• Description: activating transcription factor 1 [Source:HGNC Symbol;Acc:783]

Sequence

>retro_shar_635
AGAGATAAGAAAGAAGACAGGCAAAACCCTGGAGTTTCAACTGTCTCATCTATGTCTGTTTAACTACTATCTAGCAGACT
AGCACTGAACAGGACATTGTCATTGCCCAAAATGGAAAGTCACAACTGGCCAATATAAGCACAGATGAAGTAGAGGGGCT
GCAGGCATGAACAATGACAAATGCAGGTAATACTCAACACGAAACAGTAATTCTTCAGTGTGCACAGACAGCTGATAGAC
AGCAGATACCTATCCCAAGCAACCAAGTGGTGGTGTAGACTGCATCAGGAGATATGCAGACTTAGCAGATTCCTGTCCCA
TCCACAAATACTAACTTTCCACAGACAATGCTGATAACATCTCCAGTCATTCTAACATATCAGACAACCAAAACAGATGA
TTCACAGTTGAAAAGAGAAATAAGATTGATGAAAAAATAGAGAAGTTGCTTGAGAATGCAATAGAAAGAAAAAAGAATAT
ATTAAGTGTCTGGGAAATCAAGTTGCAGTCTTA

Alignment

ORF - retro_shar_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.36 %
• Parental protein coverage: 63.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDRKGDAESPGVSTVTSMSV-PTPIYQTSTGQYIAIAPNGTLQLASPSTEAVQGLQALTMTNASNTQQGT
          RD.K.D...PGVSTV.SMSV..T.I.QTST.Q.I.IA.NG..QLA..ST..V.GLQA.TMTNA.NTQ..T
Retrocopy RDKKEDRQNPGVSTVSSMSV<LTTI*QTSTEQDIVIAQNGKSQLANISTDEVEGLQA*TMTNAGNTQHET

Parental  TILQYAQTSDGQQILVPSNQVVVQTASGDMQTYQIRATPANTNLPQTVVMTSPVTLTSQTTKTDDPQMKR
          .ILQ.AQT.D.QQI..PSNQVVV.TASGDMQT.QI.....NTN.PQT...TSPV.LT.QTTKTDD.Q.KR
Retrocopy VILQCAQTADRQQIPIPSNQVVV*TASGDMQT*QIPVPSTNTNFPQTMLITSPVILTYQTTKTDDSQLKR

Parental  EIRLM-KNREAARECRRKKKEYVKCLENRVAVL
          EIRLM.KNRE.A.EC.RKKKEY.KCL.N.VAVL
Retrocopy EIRLM>KNREVA*ECNRKKKEYIKCLGNQVAVL

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_635 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 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004733	5 retrocopies	retro_chof_1987, retro_chof_2305, retro_chof_27, retro_chof_462, retro_chof_760,
Erinaceus europaeus	ENSEEUG00000008000	2 retrocopies	retro_eeur_332, retro_eeur_704,
Felis catus	ENSFCAG00000013892	1 retrocopy	retro_fcat_1284,
Homo sapiens	ENSG00000123268	1 retrocopy	retro_hsap_3633,
Microcebus murinus	ENSMICG00000003301	1 retrocopy	retro_mmur_1336,
Mus musculus	ENSMUSG00000023027	1 retrocopy	retro_mmus_3609,
Oryctolagus cuniculus	ENSOCUG00000017023	1 retrocopy	retro_ocun_383,
Otolemur garnettii	ENSOGAG00000026029	1 retrocopy	retro_ogar_1378,
Procavia capensis	ENSPCAG00000010038	2 retrocopies	retro_pcap_303, retro_pcap_442,
Sarcophilus harrisii	ENSSHAG00000004637	2 retrocopies	retro_shar_221, retro_shar_635 ,