RetrogeneDB ID: retro_shar_649

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856928.1:694489..694741(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS11
• Ensembl ID: ENSSHAG00000004991
• Aliases: None
• Description: ribosomal protein S11 [Source:HGNC Symbol;Acc:10384]

Sequence

>retro_shar_649
ACAGAGCATGCCTACCAGAAACAGTTAGTGATCATTCAGGACAAGAGGTAGGACTGTTCAGGAATACAAACAAAAAGATT
ATTCTAATATAATATGAAAAACATTAGGCTCCACTTCAAGACAACCAGGAAAGCCACTGAGGGCACCTAGATTGGCAAGA
AATGTCCCTTCACAGGCATTATTTCCTCCATTCAACATAGAATTATGTCAGATACAGTGATCAAGATGAAGATGCAGAGG
ATTATTGTAATC

Alignment

ORF - retro_shar_649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.76 %
• Parental protein coverage: 52.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TERAYQKQPTIFQNKKRVLLGDTAKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNV-SIRGRILS
          TE.AYQKQ..I.Q.K.....G...K.......KNI.L.FKT...A.EGT.I.KKCPFTG...SI..RI.S
Retrocopy TEHAYQKQLVIIQDKR*DCSGIQTKRLF*YNMKNIRLHFKTTRKATEGT*IGKKCPFTGIISSIQHRIMS

Parental  GVVTKMKMQRTIVI
          ..V.KMKMQR.IVI
Retrocopy DTVIKMKMQRIIVI

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_649 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 17 parental genes, and 100 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014020	13 retrocopies	retro_amel_1038, retro_amel_1071, retro_amel_1398, retro_amel_1406, retro_amel_1475, retro_amel_246, retro_amel_262, retro_amel_317, retro_amel_64, retro_amel_757, retro_amel_759, retro_amel_764, retro_amel_859,
Bos taurus	ENSBTAG00000013924	5 retrocopies	retro_btau_1282, retro_btau_1369, retro_btau_1499, retro_btau_1529, retro_btau_888,
Canis familiaris	ENSCAFG00000003631	9 retrocopies	retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955, retro_cfam_2121, retro_cfam_248,
Callithrix jacchus	ENSCJAG00000000069	1 retrocopy	retro_cjac_340,
Danio rerio	ENSDARG00000053058	1 retrocopy	retro_drer_15,
Equus caballus	ENSECAG00000000370	1 retrocopy	retro_ecab_868,
Felis catus	ENSFCAG00000009196	13 retrocopies	retro_fcat_1362, retro_fcat_1491, retro_fcat_1535, retro_fcat_1564, retro_fcat_1719, retro_fcat_1945, retro_fcat_197, retro_fcat_1991, retro_fcat_273, retro_fcat_507, retro_fcat_792, retro_fcat_854, retro_fcat_995,
Macropus eugenii	ENSMEUG00000008649	2 retrocopies	retro_meug_1176, retro_meug_1640,
Monodelphis domestica	ENSMODG00000013434	7 retrocopies	retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Otolemur garnettii	ENSOGAG00000004627	7 retrocopies	retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Pelodiscus sinensis	ENSPSIG00000011089	1 retrocopy	retro_psin_35,
Pan troglodytes	ENSPTRG00000011299	1 retrocopy	retro_ptro_88,
Rattus norvegicus	ENSRNOG00000020595	18 retrocopies	retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Sorex araneus	ENSSARG00000003236	2 retrocopies	retro_sara_11, retro_sara_469,
Sarcophilus harrisii	ENSSHAG00000004991	1 retrocopy	retro_shar_649 ,
Ictidomys tridecemlineatus	ENSSTOG00000023443	2 retrocopies	retro_itri_1033, retro_itri_805,
Tupaia belangeri	ENSTBEG00000016677	16 retrocopies	retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,