RetrogeneDB ID: retro_amel_1262

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193124.1:858057..858694(+)
• Located in intron of: ENSAMEG00000012925

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSAMEG00000000670
• Aliases: None
• Description: ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]

Sequence

>retro_amel_1262
TCCTGGGACGGGCTGTACGAAGCAGTGCGGCGGAAAGTCCTGCCCAGCAGCCAGCACAAGCACCGGAAGTTTTCAGACAC
TGTGGAGCTGCAAATCAGCTTGAAGAACTATGAACCTCAGAAGGACAAACGGTCCTTGGGCACCATCAGGCTTAAGTCTC
CTCCCTGCCCCAAGTTCTTCATGTGTGACTTAGGGGACCAGCAGTACTGTGATGAGGCCAAGGCTGTGGATATCCCCCAC
ATGAGCACAGAGGCACTGAAGACTCAACAACAATAAAAAATTAGTCAATAAGTTGTCCAAGAGGAATGATGCCTTTTCAG
CTTCAGAATCTCTGATCGAGCAGATCCCATGAATTCTGGGCCTGGGCCTGAATATGGCTGGCAGGTTCCCTTGTTGCTGA
CCCACAATGAGATCATGGTGGCCAAAAGTGGATGAAGTGAAGTCCACAATCGAATTCCAGATGAAGAAGGTGCTGTGTCT
GGCAGTGGCCGTTTTCCACGTGAAGAAGACAGATAACGGGCTTGTGTACAATGTCCACTTAGCTGTCAGTTTCCTGGTGT
CATTGCTCAAGAGGAATTGGCAGAACATCTGGGCTTTATACATCAAGAGCATCATGGGCAAGCCCCAGCGCCTGTAC

Alignment

ORF - retro_amel_1262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 97.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SRDTLYEAVR-EVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQQHC
          S.D.LYEAVR..VL...Q.K.RKF..TVELQISLKNY.PQKDKR..GT.RLKS.P.PKF..C.LGDQQ.C
Retrocopy SWDGLYEAVRRKVLPSSQHKHRKFSDTVELQISLKNYEPQKDKRSLGTIRLKSPPCPKFFMCDLGDQQYC

Parental  DEAKAVDIPHMDIEALKKL-NKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPS-LLTHNE
          DEAKAVDIPHM..EALK...N..K.LV.KL.K..DAF.ASESLI.QIP.ILG.GLN.AG.FP..LLTHNE
Retrocopy DEAKAVDIPHMSTEALKTQ>NNKK-LVNKLSKRNDAFSASESLIEQIP*ILGLGLNMAGRFPC<LLTHNE

Parental  NMVA-KVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG
          .MVA.KVDEVKSTI.FQMKKVLCLAVAV.HVK.TD..LVYN.HLAV.FLVSLLK.NWQN..ALYIKS.MG
Retrocopy IMVA>KVDEVKSTIEFQMKKVLCLAVAVFHVKKTDNGLVYNVHLAVSFLVSLLKRNWQNIWALYIKSIMG

Parental  KPQRLY
          KPQRLY
Retrocopy KPQRLY

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_1262 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1262 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 14 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000670	13 retrocopies	retro_amel_1144, retro_amel_1223, retro_amel_1262 , retro_amel_1591, retro_amel_1813, retro_amel_198, retro_amel_318, retro_amel_320, retro_amel_417, retro_amel_520, retro_amel_609, retro_amel_710, retro_amel_970,
Echinops telfairi	ENSETEG00000013325	2 retrocopies	retro_etel_1974, retro_etel_326,
Felis catus	ENSFCAG00000012904	7 retrocopies	retro_fcat_1144, retro_fcat_1488, retro_fcat_1561, retro_fcat_1971, retro_fcat_210, retro_fcat_262, retro_fcat_560,
Homo sapiens	ENSG00000198755	13 retrocopies	retro_hsap_142, retro_hsap_1462, retro_hsap_1710, retro_hsap_177, retro_hsap_1935, retro_hsap_2795, retro_hsap_3025, retro_hsap_3245, retro_hsap_3353, retro_hsap_337, retro_hsap_3949, retro_hsap_4025, retro_hsap_4040,
Gorilla gorilla	ENSGGOG00000028140	10 retrocopies	retro_ggor_1, retro_ggor_1124, retro_ggor_1282, retro_ggor_1407, retro_ggor_2088, retro_ggor_2273, retro_ggor_234, retro_ggor_2702, retro_ggor_358, retro_ggor_57,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Macaca mulatta	ENSMMUG00000015907	6 retrocopies	retro_mmul_1931, retro_mmul_2041, retro_mmul_2321, retro_mmul_2330, retro_mmul_306, retro_mmul_583,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Nomascus leucogenys	ENSNLEG00000008650	13 retrocopies	retro_nleu_1174, retro_nleu_1210, retro_nleu_1697, retro_nleu_1778, retro_nleu_1980, retro_nleu_2055, retro_nleu_2342, retro_nleu_2436, retro_nleu_2879, retro_nleu_662, retro_nleu_838, retro_nleu_986, retro_nleu_989,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Oryctolagus cuniculus	ENSOCUG00000004065	2 retrocopies	retro_ocun_130, retro_ocun_4,
Rattus norvegicus	ENSRNOG00000000505	4 retrocopies	retro_rnor_2302, retro_rnor_37, retro_rnor_400, retro_rnor_43,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Tursiops truncatus	ENSTTRG00000009431	6 retrocopies	retro_ttru_100, retro_ttru_1137, retro_ttru_1325, retro_ttru_1477, retro_ttru_205, retro_ttru_494,