RetrogeneDB ID: retro_amel_1650

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193842.1:76781..78124(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000004819
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000000348
• Aliases: None
• Description: None

Sequence

>retro_amel_1650
ATGAGTGCTTCAGTTCCCCAGTTTGAAATGTCCACACTCTATGTCGGAGACCTGCACCCCGAAGTGAATGAGGCAATGCT
GTATGAGAAATTCAGTTCTGCTGGGCCAATCCTTTCAATTCGGATGTGCCGTGATCTGCTAACACGCCGCTCTCTGGGCT
ACGCTTATGTGAACTTCTTGGTGCGGGCCAATGCTGAGTGGGCTCTGGACACAATGAACTTTGATATTATCAATGGCAAG
CCACTGCGTATTTTGTGGTCCCAGCGTGACCCATCACTTGGTAAGAGTGGAGTGGGCAATATATTCATCAGAAATCTTGC
CAACTCTATTGATAATAAGTCCCTTTATGATACATTTTCTGTCTTTGGAAACATTGTTTCTTGTAAAGTAGTAACCGATG
AAAACGGATCAAGGGGTTTTGGATTTGTGCATTTTGAGAAATCAGAAGCCGCTAAAAGGGCCATTGCAAAGATGAATGGC
ATTCTGCTGAAAGGTAGCCAAGTTTTTCTTGGGCAGTTTAAACCTCGCAAAGTAAGGGAAGCAGAGCTCAGAGCTAAAGC
AAACATATTTACCAATGTTTACGTCAAGAATTTTGGAGATGATGTAGACGATGAATGTCTTAAAGAGGTTTTTGGTGAGT
TTGGTTCTGTATTAAGTGTAAGAGTTACGATTGATGAAAGTGGAAAATCCAAAGGCTTTGGATTCGTGAATTTTGAGAAT
TTTGAAGATGCCAAGAAAGCCATTGAAGGGATGAATGGAAAGGTCCTTAACGGAAATCAAGTTTATGTTTATAGAGCCCA
AAAAAACTAGAGAGACAATCTGAACTAAAACATAAATTTGAACAAATAAAACAGTGTAAACTCACTAAATGCAAGGGTGC
TAACCTTTATGTGAAAAATCTTGAAGATGATATTGATGACAAACCACTGAGAAGAGAATTCTCCCTCTTTGGCACAATCT
ATAGTGCCAGGGTCATGATGGAGGCAGGCCACAGAAAAGGCTTTGGTTTTGTTTGCTACACAACTCCTGAGGAAGCTAAT
AAAGCTGTCATGGCAATGAATGGAAAAATTGTGATCACCAAACCACTGTATGTAGCTATTGCACAAGGTAAGGATGAGCG
CCAGGCTTTCCTCACCAAGAACTATATGGAAAGAATCTCAGCTGTGAGAGATGGAGATAATCCTATACTCAACTATCGCA
AGATAACATCATCCAATAACATCATACCAATGCTTCCTCAGTCTCAATGTGGCAGTGCACATCTTTGCAAGCCTGTGGTA
AGGGCCAAATATCATCCATCTCAGAATATACATTATGCTATCCACTCAGCAACACCTAAGCCA

Alignment

ORF - retro_amel_1650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64. %
• Parental protein coverage: 70.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRICRDKITRRSLGYAYVNYQQPVDAKRALE
          M..S.P...M..LYVGDLHP.V.EAMLYEKFS.AGPILSIR.CRD..TRRSLGYAYVN......A..AL.
Retrocopy MSASVPQFEMSTLYVGDLHPEVNEAMLYEKFSSAGPILSIRMCRDLLTRRSLGYAYVNFLVRANAEWALD

Parental  TLNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          T.NFD.I.GKP.RI.WSQRDPSL.KSGVGNIFI.NL..SIDNK.LYDTFS.FGNI.SCKVV.DENGS.G.
Retrocopy TMNFDIINGKPLRILWSQRDPSLGKSGVGNIFIRNLANSIDNKSLYDTFSVFGNIVSCKVVTDENGSRGF

Parental  GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
          GFVHFE..EAA.RAI.KMNG.LL....VF.G.FK.RK.REAEL.A.A..FTNVY.KNFG.D.DDE.LK..
Retrocopy GFVHFEKSEAAKRAIAKMNGILLKGSQVFLGQFKPRKVREAELRAKANIFTNVYVKNFGDDVDDECLKEV

Parental  FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQ-KKVERQTELKRK
          FG.FG..LSV.V..DESGKSKGFGFV.FE..EDA.KA...MNGK.LNG.Q.YV.RAQ.KK.ERQ.ELK.K
Retrocopy FGEFGSVLSVRVTIDESGKSKGFGFVNFENFEDAKKAIEGMNGKVLNGNQVYVYRAQ<KKLERQSELKHK

Parental  FEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKA
          FEQ.KQ...T...G.NLYVKNL.D.IDD..LR.EFS.FGTI.SA.VMME.G..KGFGFVC...PEEA.KA
Retrocopy FEQIKQCKLTKCKGANLYVKNLEDDIDDKPLRREFSLFGTIYSARVMMEAGHRKGFGFVCYTTPEEANKA

Parental  VTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNR
          V..MNG.IV.TKPLYVA.AQ.K.ERQA.LT..YM.R...VR...NP..N.Y.....S.......PQ.Q..
Retrocopy VMAMNGKIVITKPLYVAIAQGKDERQAFLTKNYMERISAVRDGDNPILN-YRKITSSNNIIPMLPQSQCG

Parental  AAYY-PPSQIAQLRPSP--RWTAQGARPHP
          .A....P...A...PS.........A.P.P
Retrocopy SAHLCKPVVRAKYHPSQNIHYAIHSATPKP

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_1650 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1650 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 19 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650 ,
Ailuropoda melanoleuca	ENSAMEG00000004054	1 retrocopy	retro_amel_454,
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,