RetrogeneDB ID: retro_shar_561

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849909.1:189607..190158(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3H
• Ensembl ID: ENSSHAG00000014977
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit H [Source:HGNC Symbol;Acc:3273]

Sequence

>retro_shar_561
TTTATCACTTGTGCTCTCCTGGATTCACAATATGCAATTGAAGTTCTCATTTACAATCCCATTAAAAGCTGTTCAAGAGT
CTCTATCATTGAAAACATAAACAGATTCCCAAGTTGATAGAATTTTATAAAAAGAAAGATTTTTCTCCTGAAACATTGAA
AAAAGCAAATAGCACCTTTGAACATGTTTGAAGAAGTAATGATTATAATTAAAAATTCACATCTTATCAATGTACTAATG
TGGAAACTAGAAAAGAAATCAGCTGTGGCAGATAAACACAAATTGCTCAGTCTAGCAAACAGTAATCATCTGGGGAAGAA
TCTGCAATTGTTGACAGATAGAATGGAAGAAATGAGCCAGGATATTGTTAAATTTTCTAAATGAGAAAGGACAGTTAATA
GCAACAACAGAAACATCAGTATCAGCAATACTGTCAACATCAGAATCTATAGTCCCAGAGCTGAGGAGAACCTCCTGAAG
AAGACAAATCCTAAGTTTTCAAACCTCTTCAGCCACCTTCCAGGATGGAATTGCTTCTTATTGCAGGCCAA

Alignment

ORF - retro_shar_561 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 55.24 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FVTRALLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEHM
          F.T.ALLDS....Q.AIE...VLIY.PIK..............P......K.K.F.....KK..I....M
Retrocopy FITCALLDS----QYAIE---VLIYNPIKSCSRVSIIENINRFPS**NFIKRKIFLLKH*KK-QIAPLNM

Parental  FEEVPIIIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLGKSLQLLMDRVDEMSQDIVKYNTYMRNT
          FEEV.IIIKNSHLINVLMW.LEKKSAVADKH.LLSLA.SNHLGK.LQLL.DR..EMSQDIVK.....R..
Retrocopy FEEVMIIIKNSHLINVLMWKLEKKSAVADKHKLLSLANSNHLGKNLQLLTDRMEEMSQDIVKFSK*ERTV

Parental  SK-QQQQKHQYQQRRQQENLQRQSRGEPPLPEEDMSKLFKPLQPPARMESLLIAGQ
          ...QQ.QKHQYQQ..Q..NL..QS.GEP..PEED.S..FKPLQPP.RME.LLIAGQ
Retrocopy NS<QQ-QKHQYQQYCQHQNL*SQS*GEP--PEEDKS*VFKPLQPPSRMELLLIAGQ

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_561 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561 ,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420,