RetrogeneDB ID: retro_shar_221

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834696.1:940508..941006(+)
• 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_221
CAGTCACATACTGGACAATACAATGTTATTGCCCCAAATGGAACATTATAGCTGGACAGTCCAAGCACAGAGGCAGTACA
GGGGTTACAGGCATTAACAATGACAAATGCAAGCAATACTCAACAAGGAACAATTCTTCAATATGCACAAATATATGATG
GACAGCAGATACCTAGCAACCAAGTGGTTGTACAGACTGCATCAGGAGATATGCAGACTTATCAGATTTGTGCCACACCA
GCAAATACTAATCTTCCACAGACAGTAGTGATGACATCTCCAGTCACTCTAACATCTCAGACAACCAAAACATATGATCC
ACAGATGAAAAAAGAAATAAGATTGATGAAAAATAGAGAAGCTGCTTGAGAATGCCGTAGAAAGAAAAAAGAATATGTTA
AGTGTCTGGAAAATTGAGTTGCAGTCTTGGAAAATCAAAATAAAATTTTAATAGAAGAATTTAAAACTTTAAAATATCTC
AACTCCCATAAAAATGTT

Alignment

ORF - retro_shar_221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.17 %
• Parental protein coverage: 62.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTSTGQYIAIAPNGTLQLASPSTEAVQGLQALTMTNASNTQQGTTILQYAQTSDGQQILVPSNQVVVQTA
          Q..TGQY..IAPNGTL.L.SPSTEAVQGLQALTMTNASNTQQGT.ILQYAQ..DGQQI..PSNQVVVQTA
Retrocopy QSHTGQYNVIAPNGTL*LDSPSTEAVQGLQALTMTNASNTQQGT-ILQYAQIYDGQQI--PSNQVVVQTA

Parental  SGDMQTYQIRATPANTNLPQTVVMTSPVTLTSQTTKTDDPQMKREIRLMKNREAARECRRKKKEYVKCLE
          SGDMQTYQI.ATPANTNLPQTVVMTSPVTLTSQTTKT.DPQMK.EIRLMKNREAA.ECRRKKKEYVKCLE
Retrocopy SGDMQTYQICATPANTNLPQTVVMTSPVTLTSQTTKTYDPQMKKEIRLMKNREAA*ECRRKKKEYVKCLE

Parental  NRVAVLENQNKTLIEELKTLKDLYSHKNV
          N.VAVLENQNK.LIEE.KTLK.L.SHKNV
Retrocopy N*VAVLENQNKILIEEFKTLKYLNSHKNV

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_221 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,