RetrogeneDB ID: retro_amel_1659

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193888.1:116186..117090(+)
• Located in intron of: ENSAMEG00000017087

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA4
• Ensembl ID: ENSAMEG00000012576
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 4 [Source:HGNC Symbol;Acc:14885]

Sequence

>retro_amel_1659
TTTAGAGGAGGAGGAAGGATGCAGAGAGAAAGAAGAGGTAAAAATATTGTGCATCAGCTCTCAGTAATCTTAGAAGATTT
ATATAATGGTGCAACAAGAAAACTAGCTCTGCAAAAGAATGATTTGCAAAAAATGTAAAGGCTGAGGTGGTAAGAAAAGA
GCAGAATGTTGTCCCAGTTGTGGAGGTACTGGAAAGCAAATAAGAATTCATCACATAGGACCTGGAATGGTTCAGCAATT
CAATCTGTGTGCATGGAGTGCCAGGGCCAGGGGGAACAGATCAGTCCTAAAGATCGATGTGAGAAGCTGCAATGGAAGGA
AGATAGTTTGAGAGAAGATTCTAGAAGTTCATATTGACAAAGGTATGAAAGATGGCCAGAAGATAACATTCCATGGTGAA
GGAGACCAAGAACCAGGACTGGAAACAAGAGATATATTACCATTGCTCTAGGTCAGAAGGGCCATGCTGCTTTTACTCAG
CGAAGAGAAGACCTTTTCATGTGTATGGACATATAGCTGGTTGAAGCACTGTGCAGCTTTCAAAAGCCGATATCTATTTT
TGACAACCCAACCATCATCATCACTGCTCATCCAGGTCAGACTGTCAAGCATGGAGATGTCAGTGTGCTAAATGAAGGCA
TGCCAATTTATTGTAGACCGTATGAGAAGGGTTGCCTAATCATCAAATTTAAGGTAAACTTTCCTGAGAACGGCTTTCTC
TCTCCTGATAAACTCTCTTTGCTGGAGAAACTCCTACCCAAGAGGAAGTAGAAGAGACTGATGAAACAGACCAGGTAGAA
CTGGTGGACTTTGATCCAAATCAGGAAAGACCGTACCATTACAATGGGGACGCATGTGAGGATGACGAATATCACCATAG
GGTGGTGTTCAATGTCAGACCTCT

Alignment

ORF - retro_amel_1659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.32 %
• Parental protein coverage: 75.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  FGGGGRMARERRGKNVVHQLSVTLEDLYNGVT-KKLA-LQKNVICEKCEGVGGKKGSVEKCPLCRGRGMQ
          F.GGGRM.RERRGKN.VHQLSV.LEDLYNG.T.KK...L.K..IC.KC.G.GGKK...E.CP.C.G.G.Q
Retrocopy FRGGGRMQRERRGKNIVHQLSVILEDLYNGAT<KKTS<LCKRMICKKCKG*GGKKRA-ECCPSCGGTGKQ

Parental  THVQQIGPGVVQQ-IQTVCIECKGQGERINPKDRCD-SCSGAKVIREKKIIEVHVEKGMKDGQKILFHGE
          .....IGPG.VQQ.IQ.VC.EC.GQGE.I.PKDRC..SC.G.K...EK.I.EVH..KGMKDGQKI.FHGE
Retrocopy IRIHHIGPGMVQQ<IQSVCMECQGQGEQISPKDRCE>SCNGRKIV*EK-ILEVHIDKGMKDGQKITFHGE

Parental  GDQEPELEPGDV-ITV-LDQKDHSVFQRRGHDLITKMKIQLSEALCGFKKTIKTLDDRILVITSKSGEVI
          GDQEP.LE..D..IT..L.QK.H..F..R..DL...M.I.L.EALC.F.K.I...D.....IT...G...
Retrocopy GDQEPGLETRDI<ITIALGQKGHAAFTQRREDLFMCMDI*LVEALCSFQKPISIFDNPTIIITAHPGQTV

Parental  KHGDLRCVRNEGMPIYKAPLEKGTLIIQFLVIFPEKHWLPADKLPQLEALLPPRQK-VRVTDDMDQVELK
          KHGD...V.NEGMPIY..P.EKG.LII.F.V.FPE...L..DKL..LE.LL.P..K.V..TD..DQVEL.
Retrocopy KHGDVS-VLNEGMPIYCRPYEKGCLIIKFKVNFPENGFLSPDKLSLLEKLL-PKRK<VEETDETDQVELV

Parental  EFNPS-EQNWRQHREAYEEDD-DGPRAGVQCQTA
          .F.P..E........A.E.D....P..GVQCQT.
Retrocopy DFDPNQERPYHYNGDACEDDE<ISP*GGVQCQTS

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_1659 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1659 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 11 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Ailuropoda melanoleuca	ENSAMEG00000012576	1 retrocopy	retro_amel_1659 ,
Dipodomys ordii	ENSDORG00000005972	4 retrocopies	retro_dord_245, retro_dord_280, retro_dord_333, retro_dord_533,
Echinops telfairi	ENSETEG00000004320	4 retrocopies	retro_etel_1010, retro_etel_1031, retro_etel_1067, retro_etel_608,
Macropus eugenii	ENSMEUG00000015982	4 retrocopies	retro_meug_1059, retro_meug_1893, retro_meug_292, retro_meug_624,
Microcebus murinus	ENSMICG00000008789	6 retrocopies	retro_mmur_1242, retro_mmur_1460, retro_mmur_39, retro_mmur_482, retro_mmur_496, retro_mmur_578,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
Otolemur garnettii	ENSOGAG00000006752	5 retrocopies	retro_ogar_1760, retro_ogar_1985, retro_ogar_221, retro_ogar_2656, retro_ogar_841,
Ochotona princeps	ENSOPRG00000007594	1 retrocopy	retro_opri_1028,
Tupaia belangeri	ENSTBEG00000009268	9 retrocopies	retro_tbel_2276, retro_tbel_2308, retro_tbel_2790, retro_tbel_2831, retro_tbel_3242, retro_tbel_4322, retro_tbel_4735, retro_tbel_772, retro_tbel_796,
Tarsius syrichta	ENSTSYG00000008600	1 retrocopy	retro_tsyr_1752,