RetrogeneDB ID:

retro_amel_417

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL192432.1:2415087..2415731(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL10A
Ensembl ID:ENSAMEG00000000670
Aliases:None
Description:ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]


Retrocopy-Parental alignment summary:






>retro_amel_417
AGCAAAGTGTCCTGTGACACCCTTTACAAGGCAGTGCAGGAGTCCCACACAGGAACCAGTGGAAGCACCAGAAGTTTTTG
GACACCATGGAGTAGCAGATCAACTTGAAGAACTATGATGCTCAGAATGACAAATGCTTCTTGGGCACCATCAGGCTTAA
GTTCATTCCCTGCCCCAAGTTCTCTGTGTGTGTTGTGGGGGACCAGCAGCACTATGATAAGGCCAAGCTGTGGATATCTC
CCACGTGGACATTGAAACATCAAAGAACCTCAACAAGAATAACAAATTCGTCAAGATGTTGGTCAAGAAGTACGATGCCT
TTTTGGCTTTGGAATATCTGATCAAGCAGATCCCATGAATCCTGGGCCGAGGCCTGAATAAGTCTGGCAAGTTTCCTTCT
TTACTGACCCAAAATAAGAACATGGTGGCCAAAGTTGATGAAGTGAAGTCTCATAATCAAATTCTAAATGAGGAAGGTGT
TGTGTCTGGCAGCAGAAATTGGCCACACATAGATGATAAATGATGGGCTTTTGTACAATGTCTGCTTAGCTGTCAATTTT
CTCGTGTCATTGTTCAAAAAGAATTGGCAGAATGTCTGGGCTTTATACATTAAGAGCACCATGGGCAAGCCCCAGTGCTT
ACAC

ORF - retro_amel_417 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.48 %
Parental protein coverage: 99.08 %
Number of stop codons detected: 4
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalSKVSRDTLYEAVRE-VLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ
SKVS.DTLY.AV.E.V.H.NQ.K..KFL.T.E.QI.LKNYD.Q.DK.F.GT.RLK..P.PKFSVCV.GDQ
RetrocopySKVSCDTLYKAVQE<VPHRNQWKHQKFLDTME*QINLKNYDAQNDKCFLGTIRLKFIPCPKFSVCVVGDQ
ParentalQHCDEAK-AVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTH
QH.D.AK.AVDI.H.DIE..K.LNKN.K.VK.L.KKYDAFLA.E.LIKQIP.ILG.GLNK.GKFPSLLT.
RetrocopyQHYDKAK<AVDISHVDIETSKNLNKNNKFVKMLVKKYDAFLALEYLIKQIP*ILGRGLNKSGKFPSLLTQ
ParentalNENMVAKVDEVKS-TIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKST
N.NMVAKVDEVKS..IKF.M.KVLCLA...GH..M..D.L.YN..LAVNFLVSL.KKNWQNV.ALYIKST
RetrocopyNKNMVAKVDEVKS>IIKF*MRKVLCLAAEIGHT*MINDGLLYNVCLAVNFLVSLFKKNWQNVWALYIKST
ParentalMGKPQRLY
MGKPQ.L.
RetrocopyMGKPQCLH

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_417 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_417 was not experimentally validated.

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.
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 ENSETEG000000133252 retrocopies
retro_etel_1974, retro_etel_326,
Felis catus ENSFCAG000000129047 retrocopies
retro_fcat_1144, retro_fcat_1488, retro_fcat_1561, retro_fcat_1971, retro_fcat_210, retro_fcat_262, retro_fcat_560,
Homo sapiens ENSG0000019875513 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 ENSGGOG0000002814010 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 ENSMEUG000000057606 retrocopies
retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Macaca mulatta ENSMMUG000000159076 retrocopies
retro_mmul_1931, retro_mmul_2041, retro_mmul_2321, retro_mmul_2330, retro_mmul_306, retro_mmul_583,
Monodelphis domestica ENSMODG000000137662 retrocopies
retro_mdom_276, retro_mdom_499,
Nomascus leucogenys ENSNLEG0000000865013 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 ENSOANG000000145741 retrocopy
retro_oana_86,
Oryctolagus cuniculus ENSOCUG000000040652 retrocopies
retro_ocun_130, retro_ocun_4,
Rattus norvegicus ENSRNOG000000005054 retrocopies
retro_rnor_2302, retro_rnor_37, retro_rnor_400, retro_rnor_43,
Sarcophilus harrisii ENSSHAG000000020471 retrocopy
retro_shar_438,
Tursiops truncatus ENSTTRG000000094316 retrocopies
retro_ttru_100, retro_ttru_1137, retro_ttru_1325, retro_ttru_1477, retro_ttru_205, retro_ttru_494,


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