RetrogeneDB ID: retro_amel_1142

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192952.1:240476..240795(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS20
• Ensembl ID: ENSAMEG00000006087
• Aliases: None
• Description: ribosomal protein S20 [Source:HGNC Symbol;Acc:10405]

Sequence

>retro_amel_1142
ACACTGGAAAGACCTGTGGAACCAGAGGTGGTGGGTCACTGAGTTGGAATCACCATAACCATTAGTGATGTAAAATCCCT
GGAGAAGGTGTGTACTGACCTGACCAGAGGTGCAAAGAAAAGAACCTTAAAGTGAAAGAACTGGTTCGGATGCCTACCGA
GGACTGAGAATCACTGTGAGAAAAACTTGTGGCAAAGCATCTAAGACATGGCAGCATTTCCAGATGAAAATCATTGACTT
GTACAATCCTTCCAAAACTGTTAAGCGCATTACTCCTGTAGGCATTGAGTTAGGAGTAGAGATGGAAGTCATTACTGCA

Alignment

ORF - retro_amel_1142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.28 %
• Parental protein coverage: 95.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGA-KEKNLKVKGPVRMPT-KTLRITTRKTPCGEG
          T...PVEPEV..H...IT.T...VKSLEKVC.DL.RGA.KEKNLKVK..VRMPT...LRIT.RKT.CG..
Retrocopy TLERPVEPEVVGH*VGITITISDVKSLEKVCTDLTRGA<KEKNLKVKELVRMPT<RGLRITVRKT-CGKA

Parental  SKTWDRFQMRIHKRLIDLHSPSEIVKQITSISIETGVEVEVTIA
          SKTW..FQM.I....IDL..PS..VK.IT...IE.GVE.EV..A
Retrocopy SKTWQHFQMKI----IDLYNPSKTVKRITPVGIELGVEMEVITA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1142 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1142 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 11 parental genes, and 117 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006087	17 retrocopies	retro_amel_1067, retro_amel_1142 , retro_amel_1146, retro_amel_1245, retro_amel_1405, retro_amel_1409, retro_amel_1442, retro_amel_1579, retro_amel_1619, retro_amel_1825, retro_amel_281, retro_amel_299, retro_amel_437, retro_amel_495, retro_amel_599, retro_amel_709, retro_amel_98,
Cavia porcellus	ENSCPOG00000011697	10 retrocopies	retro_cpor_1002, retro_cpor_1016, retro_cpor_1064, retro_cpor_1104, retro_cpor_1507, retro_cpor_404, retro_cpor_499, retro_cpor_533, retro_cpor_544, retro_cpor_717,
Loxodonta africana	ENSLAFG00000002515	8 retrocopies	retro_lafr_353, retro_lafr_378, retro_lafr_537, retro_lafr_719, retro_lafr_730, retro_lafr_851, retro_lafr_865, retro_lafr_880,
Macropus eugenii	ENSMEUG00000014171	21 retrocopies	retro_meug_100, retro_meug_1015, retro_meug_1058, retro_meug_1170, retro_meug_1313, retro_meug_1614, retro_meug_1702, retro_meug_1761, retro_meug_1777, retro_meug_1831, retro_meug_1911, retro_meug_1951, retro_meug_2065, retro_meug_2110, retro_meug_2187, retro_meug_659, retro_meug_710, retro_meug_723, retro_meug_818, retro_meug_892, retro_meug_928,
Myotis lucifugus	ENSMLUG00000029059	2 retrocopies	retro_mluc_1187, retro_mluc_546,
Macaca mulatta	ENSMMUG00000021314	1 retrocopy	retro_mmul_16,
Monodelphis domestica	ENSMODG00000009114	6 retrocopies	retro_mdom_1701, retro_mdom_1735, retro_mdom_1738, retro_mdom_1814, retro_mdom_1817, retro_mdom_1943,
Mustela putorius furo	ENSMPUG00000010452	15 retrocopies	retro_mputfur_1094, retro_mputfur_1188, retro_mputfur_1313, retro_mputfur_1366, retro_mputfur_1374, retro_mputfur_1432, retro_mputfur_238, retro_mputfur_249, retro_mputfur_320, retro_mputfur_418, retro_mputfur_424, retro_mputfur_433, retro_mputfur_620, retro_mputfur_77, retro_mputfur_819,
Nomascus leucogenys	ENSNLEG00000001214	19 retrocopies	retro_nleu_1013, retro_nleu_1343, retro_nleu_1447, retro_nleu_1566, retro_nleu_1794, retro_nleu_1798, retro_nleu_1805, retro_nleu_1818, retro_nleu_2059, retro_nleu_2159, retro_nleu_2654, retro_nleu_2659, retro_nleu_2750, retro_nleu_2786, retro_nleu_2819, retro_nleu_2843, retro_nleu_3066, retro_nleu_382, retro_nleu_41,
Pteropus vampyrus	ENSPVAG00000016402	8 retrocopies	retro_pvam_117, retro_pvam_1355, retro_pvam_1358, retro_pvam_554, retro_pvam_638, retro_pvam_660, retro_pvam_77, retro_pvam_800,
Sarcophilus harrisii	ENSSHAG00000011200	10 retrocopies	retro_shar_135, retro_shar_228, retro_shar_418, retro_shar_436, retro_shar_441, retro_shar_443, retro_shar_450, retro_shar_504, retro_shar_544, retro_shar_785,