RetrogeneDB ID: retro_amel_180

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192347.1:1644596..1645230(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSA2
• Ensembl ID: ENSAMEG00000000593
• Aliases: None
• Description: NSA2 ribosome biogenesis homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:30728]

Sequence

>retro_amel_180
CCACAGAACAAATATATTGAGTTACACCGGAAGCGCTGTGGCTACGGTTTGAATTACCATGAGGAAAAGAGAAAGAAAGA
AGGTCAAGAGGCTCATGAATGTTCAAAGAAGGCAAAAAAGCTGACTGGTCTGAAAGCTAAGCTCTACCATAAACAGCACC
ATGCTGAGAAAATACAAACGAAAAAGACAATCAAGATGTATGAAAAGAGAAGCACCAAACAAAAGACTGATGGAAAGAAT
CCACAAGGAGCAATGCCTGCATGTCTACCGGACAGGAAGGGACTGTCCTGAGCTAAAGAACTTTCCAGTATGATTAAACG
AAAACGAAAAGAGAAAGCGGGAAAATGGGAGGTCCCTTTACCCAAAGTTTGTGCCCAGGGAGAAACAGAAGTATTAAAAG
TTATTCGAACAGGAAAGAGAAAGAAGAAAGCATGGAAGAGGATGGTTACTAAAGCCCACTTTGTTGGAGATGGCTTTACT
CAAAAACCACCTAAAGATGAAAGATTCATTAAGCCAATGGGCTTACATTTCAAAAAGACCCATGTAACACAGCCTGAACT
GAAAGCCACTTTCTGCCTGCCAACACTTGGTGTAAAAAAAGAATCCCTCATCCCCACTATATACAACTTTGGGT

Alignment

ORF - retro_amel_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.49 %
• Parental protein coverage: 81.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PQNEYIELHRKRCGYRLDYHEKKRKKEGREAHERSKKAKKMIGLKAKLYHKQRHAEKIQMKKTIKMHEKR
          PQN.YIELHRKRCGY.L.YHE.KRKKEG.EAHE.SKKAKK..GLKAKLYHKQ.HAEKIQ.KKTIKM.EKR
Retrocopy PQNKYIELHRKRCGYGLNYHEEKRKKEGQEAHECSKKAKKLTGLKAKLYHKQHHAEKIQTKKTIKMYEKR

Parental  NTKQKNDEKTPQGAVPAYLLDREGQSRAKVLSNMIKQKRKEKAGKWEVPLPKVRAQGETEVLKVIRTGKR
          .TKQK.D.K.PQGA.PA.L.DR.G.S.AK.LS.MIK.KRKEKAGKWEVPLPKV.AQGETEVLKVIRTGKR
Retrocopy STKQKTDGKNPQGAMPACLPDRKGLS*AKELSSMIKRKRKEKAGKWEVPLPKVCAQGETEVLKVIRTGKR

Parental  KKKAWKRMVTKVCFVGDGFTRKPPKYERFIRPMGLRFKKAHVTHPELKATFCLPILGV-KKNPSSPLYTT
          KKKAWKRMVTK..FVGDGFT.KPPK.ERFI.PMGL.FKK.HVT.PELKATFCLP.LGV.KKNPSSPLYTT
Retrocopy KKKAWKRMVTKAHFVGDGFTQKPPKDERFIKPMGLHFKKTHVTQPELKATFCLPTLGV>KKNPSSPLYTT

Parental  LG
          LG
Retrocopy LG

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_180 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_180 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 13 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000593	5 retrocopies	retro_amel_151, retro_amel_1635, retro_amel_1729, retro_amel_180 , retro_amel_734,
Canis familiaris	ENSCAFG00000008311	4 retrocopies	retro_cfam_1292, retro_cfam_361, retro_cfam_49, retro_cfam_64,
Callithrix jacchus	ENSCJAG00000016874	1 retrocopy	retro_cjac_116,
Echinops telfairi	ENSETEG00000004095	13 retrocopies	retro_etel_1086, retro_etel_1479, retro_etel_1786, retro_etel_2030, retro_etel_2112, retro_etel_2116, retro_etel_2197, retro_etel_359, retro_etel_613, retro_etel_729, retro_etel_890, retro_etel_940, retro_etel_988,
Felis catus	ENSFCAG00000011978	1 retrocopy	retro_fcat_98,
Loxodonta africana	ENSLAFG00000009910	4 retrocopies	retro_lafr_253, retro_lafr_455, retro_lafr_620, retro_lafr_714,
Macropus eugenii	ENSMEUG00000015798	3 retrocopies	retro_meug_1191, retro_meug_1408, retro_meug_161,
Monodelphis domestica	ENSMODG00000001900	4 retrocopies	retro_mdom_115, retro_mdom_1702, retro_mdom_581, retro_mdom_592,
Mustela putorius furo	ENSMPUG00000005795	5 retrocopies	retro_mputfur_153, retro_mputfur_250, retro_mputfur_510, retro_mputfur_573, retro_mputfur_690,
Oryctolagus cuniculus	ENSOCUG00000006536	6 retrocopies	retro_ocun_149, retro_ocun_1591, retro_ocun_1602, retro_ocun_306, retro_ocun_658, retro_ocun_76,
Rattus norvegicus	ENSRNOG00000016530	15 retrocopies	retro_rnor_1074, retro_rnor_1317, retro_rnor_1366, retro_rnor_1921, retro_rnor_2630, retro_rnor_2745, retro_rnor_2767, retro_rnor_2817, retro_rnor_2820, retro_rnor_2852, retro_rnor_2877, retro_rnor_2964, retro_rnor_618, retro_rnor_945, retro_rnor_951,
Sorex araneus	ENSSARG00000009424	4 retrocopies	retro_sara_555, retro_sara_589, retro_sara_620, retro_sara_703,
Tupaia belangeri	ENSTBEG00000012978	56 retrocopies	retro_tbel_1062, retro_tbel_1078, retro_tbel_1141, retro_tbel_1317, retro_tbel_1329, retro_tbel_1476, retro_tbel_152, retro_tbel_1548, retro_tbel_1569, retro_tbel_1627, retro_tbel_1733, retro_tbel_1762, retro_tbel_1778, retro_tbel_179, retro_tbel_1845, retro_tbel_1940, retro_tbel_2102, retro_tbel_2113, retro_tbel_2138, retro_tbel_2220, retro_tbel_229, retro_tbel_254, retro_tbel_2586, retro_tbel_2757, retro_tbel_2784, retro_tbel_3016, retro_tbel_3040, retro_tbel_3116, retro_tbel_3264, retro_tbel_3298, retro_tbel_3417, retro_tbel_3514, retro_tbel_3601, retro_tbel_3650, retro_tbel_3724, retro_tbel_3736, retro_tbel_3763, retro_tbel_3795, retro_tbel_4028, retro_tbel_406, retro_tbel_4104, retro_tbel_4169, retro_tbel_4270, retro_tbel_430, retro_tbel_4401, retro_tbel_4422, retro_tbel_4491, retro_tbel_4503, retro_tbel_4513, retro_tbel_4642, retro_tbel_4689, retro_tbel_535, retro_tbel_670, retro_tbel_721, retro_tbel_897, retro_tbel_91,