RetrogeneDB ID: retro_shar_827

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867596.1:969965..970390(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TKT
• Ensembl ID: ENSSHAG00000017349
• Aliases: None
• Description: transketolase [Source:HGNC Symbol;Acc:11834]

Sequence

>retro_shar_827
AACACGAAGGGGATCTGTTTCTTAATGCCAAGCTACCCAAAGACCGCCATCATTTACTACAACAACAAAAATGTTCAGGT
TGGCCAAGCTAAGGTGATCCTCAAGAGCAAGGATGACCAGGTGACTGTGACTGGCACTGGGATGACCCTCAATGAAGCCT
TGGCAGTGGCAGAGCAGCTGAAGAAAGAAAAGCTCAACATCCAAGTACTTGGTGCCTTTACAATTAAGCTCTGGATGAGA
CACTCATCCTTGAAAGTGCCGGTGTGACTCCTGGCCACATCCTGACTGTAGAGGACCATTACTTTGAAGATGGCAGAAGA
GAGGCTGTGACTGCTGCCATAGTGGGTTAACCGAGTGCCACCATCACTCCCTGGGGGGTCACCAGCATCCAGAGCAACGG
GAAGCCGGTGGAGCTGCTGAAGATG

Alignment

ORF - retro_shar_827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.43 %
• Parental protein coverage: 54.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NTKGICFIRTSRPENAIIYNNNENFQIGQAKVVLKSKDDQITVIGAGVTLHEALAAAEQLKKEKINIRVL
          NTKGICF...S.P..AIIY.NN.N.Q.GQAKV.LKSKDDQ.TV.G.G.TL.EALA.AEQLKKEK.NI.VL
Retrocopy NTKGICFLMPSYPKTAIIYYNNKNVQVGQAKVILKSKDDQVTVTGTGMTLNEALAVAEQLKKEKLNIQVL

Parental  DPFTIK-PLDKKLILESAGATHGRILTVEDHYYEGGIGEAVASAIVGESGVTLTRLAVASVPRSGKPAEL
          ..FTIK..LD..LILESAG.T.G.ILTVEDHY.E.G..EAV..AIVG....T.T...V.S....GKP.EL
Retrocopy GAFTIK<ALDETLILESAGVTPGHILTVEDHYFEDGRREAVTAAIVG*PSATITPWGVTSIQSNGKPVEL

Parental  LKM
          LKM
Retrocopy LKM

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_827 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 19 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003758	1 retrocopy	retro_btau_176,
Callithrix jacchus	ENSCJAG00000007253	1 retrocopy	retro_cjac_2128,
Cavia porcellus	ENSCPOG00000000072	1 retrocopy	retro_cpor_45,
Dipodomys ordii	ENSDORG00000001392	1 retrocopy	retro_dord_329,
Homo sapiens	ENSG00000163931	1 retrocopy	retro_hsap_47,
Macropus eugenii	ENSMEUG00000005312	3 retrocopies	retro_meug_1397, retro_meug_160, retro_meug_796,
Myotis lucifugus	ENSMLUG00000000943	1 retrocopy	retro_mluc_67,
Macaca mulatta	ENSMMUG00000014433	1 retrocopy	retro_mmul_74,
Mus musculus	ENSMUSG00000021957	1 retrocopy	retro_mmus_220,
Oryctolagus cuniculus	ENSOCUG00000015904	2 retrocopies	retro_ocun_319, retro_ocun_62,
Otolemur garnettii	ENSOGAG00000016911	1 retrocopy	retro_ogar_5,
Ochotona princeps	ENSOPRG00000009891	1 retrocopy	retro_opri_10,
Pan troglodytes	ENSPTRG00000015024	1 retrocopy	retro_ptro_126,
Pteropus vampyrus	ENSPVAG00000016283	1 retrocopy	retro_pvam_352,
Rattus norvegicus	ENSRNOG00000016064	1 retrocopy	retro_rnor_146,
Sarcophilus harrisii	ENSSHAG00000017349	1 retrocopy	retro_shar_827 ,
Sus scrofa	ENSSSCG00000021408	1 retrocopy	retro_sscr_996,
Tupaia belangeri	ENSTBEG00000012114	1 retrocopy	retro_tbel_3510,
Takifugu rubripes	ENSTRUG00000003009	1 retrocopy	retro_trub_23,