RetrogeneDB ID: retro_shar_165

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834508.1:1328953..1329963(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA2
• Ensembl ID: ENSSHAG00000011391
• Aliases: None
• Description: karyopherin alpha 2 (RAG cohort 1, importin alpha 1) [Source:HGNC Symbol;Acc:6395]

Sequence

>retro_shar_165
GATGGTTCAGCCTACAGAGACTTAGTTGTCAAGTATGGTGCAATAGACCCTCTTTTAGCTCTTCTTGCAGTTCCTGATAT
ATCATCGTTAGCATGTGGTTACTTAAGAAATCTTACTTGGACACTTTCAAATCTTTGTCGCAACAAGAATCCTGCTCCCC
TAATAGAAGCTATTGAGCAAATTCTTCCAACCTTAGTTCGCCTTTTGCATCATGATGATCCAGAAGTTCTGGCAGATACC
TGTTGGACTATTTCCTATATCACAGATGGCTCAAATGACAGGATTGAAGTAGTTGTGAAAACAGGAGTTGTGGGACAACT
AGTCAAACATCATCTAGGATCTGTTGAATTGCCAATAGTGACTCCTTCTTTATGGGCTATAAGAAACATTGTCACTGGGA
CAAATGAACAAACTCAGATTGTAATAGATTCAGGAGTGCTTGCTGTCTTTCCTAGCCTGCTTACTCACCCCAAAACCAAT
ATCCAGAAGGAGGCTGCATGGACCATGTCAAACATCACGGCTGGCCATCAGGACCAAATACAGCAAGTTGTGAATCATGG
ACTAGTTCCATCCTTGGTTGGAATTCTGTCAGAGGGAGACTTTAAGTCACAGAAAGAAGCTATATGAGCTCTGACAAACT
ATACCAGTGGTGGAACAATTGAACAGATTGTCTATTTGTCCAAAATGAAATTCTGGAATCCTTAATCAACCCCTTGTCTG
CAAAAGACAGCAAAATAGTCCTGGTTATTTTGGATGCAATTTCAAATATTTTTCTGGCTGCTGAAAAACTAAATGAAACT
GAAAAACTTTGTATCCCAATTGAAGAATGTGGCAGGATAGACAGAATTGAAGCACTTCAGTCCCATGAAAATGAAATGGT
ATATAAAGCTTCCTCCAGCTTAATTGAAAAATATTTCTCTGCAGAGGAAGATCAAAATGTTGTACCAGAATCTATCTCTG
ATGGCTATAACTTCCAGATTCAAGATGGCACACCTGGGACCTTTAACTTT

Alignment

ORF - retro_shar_165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.97 %
• Parental protein coverage: 63.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGSAYRDLVIKYGAIDPLLALLAVPDISSLACGYLRNLTWTLSNLCRNKNPAPPIEAIEQILPTLVRLLH
          DGSAYRDLV.KYGAIDPLLALLAVPDISSLACGYLRNLTWTLSNLCRNKNPAP.IEAIEQILPTLVRLLH
Retrocopy DGSAYRDLVVKYGAIDPLLALLAVPDISSLACGYLRNLTWTLSNLCRNKNPAPLIEAIEQILPTLVRLLH

Parental  HDDPEVLADTCWAISYLTDGSNDRIEVVVKTGVVPQLVK-LLGSGELPIVTPSLRAIGNIVTGTDEQTQI
          HDDPEVLADTCW.ISY.TDGSNDRIEVVVKTGVV.QLVK..LGS.ELPIVTPSL.AI.NIVTGT.EQTQI
Retrocopy HDDPEVLADTCWTISYITDGSNDRIEVVVKTGVVGQLVKHHLGSVELPIVTPSLWAIRNIVTGTNEQTQI

Parental  VIDSGALAVFPSLLTHPKTNIQKEVAWTMSNITAGRQDQIQQVVNHGLVPYLVGILSEGDFKSQKEAVWA
          VIDSG.LAVFPSLLTHPKTNIQKE.AWTMSNITAG.QDQIQQVVNHGLVP.LVGILSEGDFKSQKEA..A
Retrocopy VIDSGVLAVFPSLLTHPKTNIQKEAAWTMSNITAGHQDQIQQVVNHGLVPSLVGILSEGDFKSQKEAI*A

Parental  VTNYPSGGTIEQIVYL-VQNGILESLINLLSAKDSKIVLVIF-AISNIFLAAEKLNETEKLCILIEECGG
          .TNY.SGGTIEQIVYL.VQN.ILESLIN.LSAKDSKIVLVI..AISNIFLAAEKLNETEKLCI.IEECG.
Retrocopy LTNYTSGGTIEQIVYL<VQNEILESLINPLSAKDSKIVLVILDAISNIFLAAEKLNETEKLCIPIEECGR

Parental  LDRIESLQSHENEMVYKASSSLIEKYFSAEEEDQNVVPESTSEGYTFQIQDGTPRSFNF
          .DRIE.LQSHENEMVYKASSSLIEKYFSA.EEDQNVVPES.S.GY.FQIQDGTP..FNF
Retrocopy IDRIEALQSHENEMVYKASSSLIEKYFSA-EEDQNVVPESISDGYNFQIQDGTPGTFNF

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_165 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 23 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus	ENSBTAG00000012225	1 retrocopy	retro_btau_1830,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus	ENSECAG00000020573	2 retrocopies	retro_ecab_1017, retro_ecab_1123,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176, retro_fcat_921,
Homo sapiens	ENSG00000182481	1 retrocopy	retro_hsap_2950,
Gorilla gorilla	ENSGGOG00000027535	2 retrocopies	retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Nomascus leucogenys	ENSNLEG00000001749	3 retrocopies	retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus	ENSOCUG00000015913	4 retrocopies	retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501,
Pteropus vampyrus	ENSPVAG00000004976	2 retrocopies	retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165 ,
Tupaia belangeri	ENSTBEG00000006274	14 retrocopies	retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos	ENSVPAG00000001855	3 retrocopies	retro_vpac_124, retro_vpac_162, retro_vpac_163,