RetrogeneDB ID: retro_shar_35

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867584.1:4490138..4491962(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000018884
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000006470
• Aliases: None
• Description: None

Sequence

>retro_shar_35
ATGGGAAGGGCTGAAAGGTCAAGAGAACTTCAGTTCCCTTCCAGTGCCCCTCCTCCCAGTCACACGTACTGCTACTTCCA
GCGTTCCAATCCTTTACTTCAGAACTCTATCTCCAGGGTACAACGTAGGTCGAGCCGAGGCACAACAGAAATGCCTGGCT
CCATGGCAGACATTGAGAAAACCGATTTGGGGCCCTTGGTCGGCGCTATCGATCAAGGGACCAGCTCCACTCGCTTTCTA
GTGTTTAATTCGACAACGGCCGAACTCCTCAGCCATCACAAAATTGAGCTGAAGCAGAAGTTTCCAAAGGAGGGCTGGGT
CGAACAAGACCCCATAGAGATCCTGCAGTCTGTCTATGACTGTATGGAGACAACATGTGAGAAGCTTAATGAGCTGAATG
TTGACATTTCTACCATCAAAGCCATCGGGCTGAGCAACCAGAGGGAGACTACTGTTATCTGGGACAAGTTTACTGGAGAG
CCTCTCTACAATGCCGTGGTTTGGCTTGATCTTCGTACCCAGTCAACGGTTCAGCTTCTCAGTAAGAAAATCCCTGGCAA
TAATAATTTTGTCAAATCAAAGACCGGGCTGCCTCTGAGCACTTACTTTAGTGCCGTGAAGCTCCACTGGCTCTTGGAAA
ATGTGAGAAAAGTTAAGAGAGCTGTCGAGGACCAAAGAGCCCTTTTTGGGACCATTGATTCCTGGGTGATCTGGAACCTG
ACCGGAGGCATCGATGGAGGGGTCCACTGTACAGATGTAACCAACGCCAGTCGAACCATGCTTTTCAACATTCACTCGCT
GAAATGGGACGTAGAGCTGTGTGAGTTTTTTGACGTTCCTATGAATATGCTTGCAGAAGTCCGCAGTTCTTCCGAGATCT
ATGGGCTGATGAAATCTGGAGCTCTGGAAGGTGTGCCAATATCCGGATGCCTGGGAGACCAGTCTGCAGCTTTGGTGGGA
CAGATGTGCTTCCAAGACGGGCAAGCCAAAAATACCTACGGAACCGGTTGCTTCTTAATGTGCAATACAGGAACAAAGTG
TGTCTTCTCTGAACATGGCCTCATCACCACTGTGGCTTACAAGCTGGGCCGAGACAAGCCAGCCATCTATGCGTTGGAAG
GATCCGTTGCCATCACCGGGGCTGTCATTCAGTGGCTGAAAGACAATCTGGGCATTATAGAAACCATAGAAGAGATCGAA
ACACTAGCCGAAGAGGCGGGATCGGCTCACGGCTGCTACTTTGTTCCAGCATTCTCAGGTTTATACGCACCATACTGGGA
ACCAACTGCAAGAGGTATTATTTGTGGACTTACTCATTTCACAAACAAACAACATATCGCCTTTGCCGCATTAGAGGCAA
TCTGTTTCCAAACCCGGGAAATAGTGGATGCTATGAATCAAGATTTTGGAACTCCACTCACCCATTTACAAGTAGACGGA
GCAATGACCAACAACAAAATTCTAATGCAACTTCAGGCAGACGTACTGAATATACCGGTAGTGAAGCCTTCGATGCCTGA
AACAGCTGCACTGGGGGCAGCCATGGCTGCTGGAGCCGCAAAAGGAGTAGACGTCTGGAGTCTGGAAGCTGATGATCTAT
CACCTGTCAACGTGGAGCAGTTTGAACCGGAGATAAATGCAGAAGAAGGTGAAAATCGCTATTCTACTTGGAAGAAAGCC
GTGCAGAGATCCATGGGCTGGGTTGTACCTCGGAGCCGTCTAAGCGGCCATTTTGATCTCATCTGCAGTATACCTCTGGG
CTTTTTTATAGTGTCTACCATTATAATGTTAATTGGAGCAAGGTACATCTCAGGGGATCCCTAA

Alignment

ORF - retro_shar_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLFNIHSLEWDIELCEFFEIPMTILPNIRSSSEIYGLMKAGALEGVPLSGCLGDQSAALVGQMCFQDGQA
          MLFNIHSL.WD.ELCEFF..PM..L...RSSSEIYGLMK.GALEGVP.SGCLGDQSAALVGQMCFQDGQA
Retrocopy MLFNIHSLKWDVELCEFFDVPMNMLAEVRSSSEIYGLMKSGALEGVPISGCLGDQSAALVGQMCFQDGQA

Parental  KNTYGTGCFLLCNTGQKCVFSDHGLLTTVAYKLGRDKPVCYALEGSVAIAGAVVRWLRDNLGIIESSEEI
          KNTYGTGCFL.CNTG.KCVFS.HGL.TTVAYKLGRDKP..YALEGSVAI.GAV..WL.DNLGIIE..EEI
Retrocopy KNTYGTGCFLMCNTGTKCVFSEHGLITTVAYKLGRDKPAIYALEGSVAITGAVIQWLKDNLGIIETIEEI

Parental  ENLAKEAGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKQHIAFAALEAVCFQTREILDAMNKDC
          E.LA.EAG...GCYFVPAFSGLYAPYWEP.ARGIICGLT.FTNKQHIAFAALEA.CFQTREI.DAMN.D.
Retrocopy ETLAEEAGSAHGCYFVPAFSGLYAPYWEPTARGIICGLTHFTNKQHIAFAALEAICFQTREIVDAMNQDF

Parental  GIPLSHLQVDGGMTNNKILMQLQADILCIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTME
          G.PL.HLQVDG.MTNNKILMQLQAD.L.IPVVKPSMPET.ALGAAMAAGAA.GV.VWSLE..DLS.V..E
Retrocopy GTPLTHLQVDGAMTNNKILMQLQADVLNIPVVKPSMPETAALGAAMAAGAAKGVDVWSLEADDLSPVNVE

Parental  RFEPQINEEESEIRYATWKKAVQKSMGWATGESPANAGDPNIFCSVPLGFFIVTSMVMLIGARYISGIP
          .FEP.IN.EE.E.RY.TWKKAVQ.SMGW....S....G.....CS.PLGFFIV....MLIGARYISG.P
Retrocopy QFEPEINAEEGENRYSTWKKAVQRSMGWVVPRSRL-SGHFDLICSIPLGFFIVSTIIMLIGARYISGDP

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_35 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 21 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009161	1 retrocopy	retro_amel_45,
Canis familiaris	ENSCAFG00000013713	1 retrocopy	retro_cfam_19,
Callithrix jacchus	ENSCJAG00000007633	3 retrocopies	retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Equus caballus	ENSECAG00000003599	1 retrocopy	retro_ecab_9,
Echinops telfairi	ENSETEG00000008279	2 retrocopies	retro_etel_2000, retro_etel_247,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Homo sapiens	ENSG00000198814	4 retrocopies	retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana	ENSLAFG00000007632	1 retrocopy	retro_lafr_30,
Myotis lucifugus	ENSMLUG00000001046	2 retrocopies	retro_mluc_151, retro_mluc_853,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Mus musculus	ENSMUSG00000025059	2 retrocopies	retro_mmus_119, retro_mmus_97,
Nomascus leucogenys	ENSNLEG00000010102	2 retrocopies	retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Otolemur garnettii	ENSOGAG00000016952	1 retrocopy	retro_ogar_261,
Pteropus vampyrus	ENSPVAG00000012460	1 retrocopy	retro_pvam_1417,
Rattus norvegicus	ENSRNOG00000034116	2 retrocopies	retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35 ,
Sus scrofa	ENSSSCG00000012202	2 retrocopies	retro_sscr_479, retro_sscr_59,
Ictidomys tridecemlineatus	ENSSTOG00000008732	1 retrocopy	retro_itri_1436,
Tarsius syrichta	ENSTSYG00000008249	1 retrocopy	retro_tsyr_29,