RetrogeneDB ID: retro_amel_1438

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193370.1:226968..227902(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NONO
• Ensembl ID: ENSAMEG00000016057
• Aliases: None
• Description: non-POU domain containing, octamer-binding [Source:HGNC Symbol;Acc:7871]

Sequence

>retro_amel_1438
AATGGACAACAAGCCAGCAGCCAAAACGAAGGCTTGACTATTGACCTGAAGAATTTTAGGAAACCAGGAGAGAAGAACTT
CACCCAACATAGCCAGCTCTTTGTGGGCAATCTTCCTCTTGATGCCACTGAGGAGGAGATGAAGAAACAACTTGAGAAAT
ACGGAATGGCCGTGAAGTCTTCATTCAGAAGGATAAGGGTTTTGGTTTTATCTGCTTGGAAACTCGAACCCGAGGGGAGA
TGGCCGAAGTAGAGCTGGACAACGTGCTGCTCCGTGGAAAGCAGCTGCCTGTGCGCTTTGCCTGCCATAGTGCATCCCTT
ACAGTCTGAAACCTCCCTCGGTGTGTTTCCAACAAACTGCCCGAGGAAGCCTTTTTGGTGTCTGGCCAGGTGGAAAGGGC
TGTTGTCCTCGTGGATGATCAAGGAAGACCCTCAGGAAAATGCACTGCTGAAGTCTCAGGGAAGCCAGCTGCTCGGAAAG
CTCTGGAAGGCTCCTTTCCGCTAACCACGTTTCCCTGGCCTGTGACTGTGGAGCCCATGGACCAGCTGGATGATGAAGAG
GGACCTCCAGAGAAGCTGGTGATAAAGAACGAGAAATTTCACCAGGAGCAGCCACCCGGCTCTGCACATCCTGGCTCCTT
TGAGTGTGAGTATGCCACATGTTGGAAGACTAGGCGCTCACTGAGATGGAGAAGCAGCAGCAGGACCAAGTGGACCGCAA
CATCAAGGAAGCTCATGAGAAGCTGGAGATGGAGCTCATGCTAATGAGACAGGATCTGATGAGGCGTCAAGAAGAACTTC
GGAGGATGGAAGAGCTGCACAACCAAGAAGTACAAAAACGAAAGCAACTGGAGCTCAGGCAGGAGGAGGAGCGCAGGCTC
CGTGAGGAGGAGGCGCAGAGGCAACAGGAAGAAATGAGGCAGCGATGGCAGGAA

Alignment

ORF - retro_amel_1438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.18 %
• Parental protein coverage: 67.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGQQASSQNEGLTIDLKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKA-GEVFIHKDKGFG
          NGQQASSQNEGLTIDLKNFRKPGEK.FTQ.S.LFVGNLP.D.TEEEM.K..EKYG.A..EVFI.KDKGFG
Retrocopy NGQQASSQNEGLTIDLKNFRKPGEKNFTQHSQLFVGNLPLDATEEEMKKQLEKYGMA<REVFIQKDKGFG

Parental  FIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVD
          FI.LETRT..E.A.VELDN..LRGKQL.VRFACHSASLTV.NLP..VSN.L.EEAF.V.GQVERAVV.VD
Retrocopy FICLETRTRGEMAEVELDNVLLRGKQLPVRFACHSASLTV*NLPRCVSNKLPEEAFLVSGQVERAVVLVD

Parental  DRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFHKERE
          D.GRPSGK...E.SGKPAARKAL.....GSF.LTTFP.PVTVEPMDQLDDEEG.PEKLVIKN..FH...E
Retrocopy DQGRPSGKCTAEVSGKPAARKALE----GSFPLTTFPWPVTVEPMDQLDDEEGPPEKLVIKNEKFH--QE

Parental  QPPRFAQPGSFEYEYAMRWKALIEM-EKQQQDQ--VDRNIKEAREKLEMEMEAARHEHQVMLMRQDLMRR
          QPP..A.PGSFE.EYA..WK......E...Q.Q..VDRNIKEA.EKLEME....R...Q....RQ...RR
Retrocopy QPPGSAHPGSFECEYATCWKTRRSL<EMEKQQQDQVDRNIKEAHEKLEMELMLMR---QDLMRRQEELRR

Parental  QEELRRMEELHNQEVQKRKQLELR-QEEERRRREEEMRRQQEE
          .EEL...E.........R...E.R..EEE..R..EEMR....E
Retrocopy MEELHNQEVQKRKQLELRQEEERRLREEEAQRQQEEMRQRWQE

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_1438 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1438 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 21 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016057	2 retrocopies	retro_amel_1438 , retro_amel_795,
Bos taurus	ENSBTAG00000012152	2 retrocopies	retro_btau_1027, retro_btau_313,
Canis familiaris	ENSCAFG00000017071	1 retrocopy	retro_cfam_98,
Callithrix jacchus	ENSCJAG00000036744	1 retrocopy	retro_cjac_3990,
Equus caballus	ENSECAG00000008502	2 retrocopies	retro_ecab_357, retro_ecab_427,
Felis catus	ENSFCAG00000014807	2 retrocopies	retro_fcat_1219, retro_fcat_147,
Homo sapiens	ENSG00000147140	1 retrocopy	retro_hsap_1699,
Gorilla gorilla	ENSGGOG00000006194	1 retrocopy	retro_ggor_1273,
Microcebus murinus	ENSMICG00000000232	1 retrocopy	retro_mmur_569,
Myotis lucifugus	ENSMLUG00000002489	1 retrocopy	retro_mluc_622,
Mustela putorius furo	ENSMPUG00000004937	1 retrocopy	retro_mputfur_937,
Mus musculus	ENSMUSG00000031311	2 retrocopies	retro_mmus_3652, retro_mmus_632,
Nomascus leucogenys	ENSNLEG00000001278	1 retrocopy	retro_nleu_1344,
Oryctolagus cuniculus	ENSOCUG00000021848	2 retrocopies	retro_ocun_1317, retro_ocun_1804,
Otolemur garnettii	ENSOGAG00000004834	3 retrocopies	retro_ogar_1525, retro_ogar_546, retro_ogar_593,
Pongo abelii	ENSPPYG00000020451	1 retrocopy	retro_pabe_1398,
Pan troglodytes	ENSPTRG00000022010	1 retrocopy	retro_ptro_1150,
Pteropus vampyrus	ENSPVAG00000016503	1 retrocopy	retro_pvam_444,
Rattus norvegicus	ENSRNOG00000003689	2 retrocopies	retro_rnor_1178, retro_rnor_1503,
Sorex araneus	ENSSARG00000007959	2 retrocopies	retro_sara_661, retro_sara_663,
Drosophila melanogaster	FBgn0004227	1 retrocopy	retro_dmel_11,