RetrogeneDB ID: retro_amel_1512

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193536.1:608127..609530(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYP51A1
• Ensembl ID: ENSAMEG00000005722
• Aliases: None
• Description: cytochrome P450, family 51, subfamily A, polypeptide 1 [Source:HGNC Symbol;Acc:2649]

Sequence

>retro_amel_1512
CTGCTGATGGCCTGAGCCTCGACGCTTGGCCTAGTCTACCTGCTCTGCCCTGCAGTCGGCCACCTGGCCCCCTGCCAACC
GCAGAGAAAAGTCCAGTGTACATTACTCTCCAACACCATTCCTTAGACAGGCCATAGCATTTGGGAAAAGTCCAACTGAA
TTCCTAGGAAATGCATGAGAAGTATGGACCTGTATTTAGTTTTACCATGGTAAGCAAGACATTTACTCACCTTCCCGGTA
GTGATGCTGCTGCACTATTTCTTAATGGTAAAAATGAAGACCTAAATGCAGACGATGTCTACAGTCACCCTACAAGACCT
GTGTTTGGGAAGGGAGTTGCACAGGATGTGTCTAACCCAGGTTTTTTTGGAGCAGAAGAAAATGTTAAAAAGTGGTCTTT
ATTTGGCCCACATTAGACAGCACGTTTCTATAAGTGAAAAGGAAACAAAAGAATACTTTCCAAGTTGGGGATAAAGTAGA
GAAAAAAATTGGTTTGAAGCTCTTCCTGAGCTCACAATTTTAACAGCCAGCCACTGCTAAGTGGAAAGGAAATCAGAAGT
CAACTCAGTGAGAGGCACAACTCTGCAGATTTGGATGGAGGTTTCAGCCTTGCGGCTGGCTGGTGCCAGGTTGGCTCCCT
TTGCCTAGTTTCAGATACAGGGACAGAGCTCATTGAGAGATCAAGAATATTTTCTGTAAAGCAATCCAGAAACACAGAGA
GTCAGTAGAAAACATTGACGACACTCTCCAAACTTTCCTAGCTTCTACTTACAAGGATGGGCATCCTTTGACAGATGATG
AGGTGGCAGGCATGCTTACGGGGCCGCTCCTGGCAGGGTGACATACGTCCTCAACCACTGGCACCTGGATGGGCTTCTTT
TTGGCCAGAGACAAAACGGTTCAAGAAAAATGTTACTTAGAAAACAGTCTGTGAAGATCTGCCTCCTTTAATTTATGACC
AGCTGAAGGATCGAAATTTCCTTGATCACTGTATAAAGGAAACATTAAGACTTTGACTTCCTATGATGACCATGATGAGA
ATGGCCAAAACTCCTCAGACGGTGACAGACTACACCATTCCTCCAGGACAGCAGGTGTGCGCTCCTCCCCCTGTCAGTCA
AAGACTTAAACACTCCTGGGTAGAACGTCTGGACTTCAATCCTGACTGCTACTTACAGGACAGTCCAGCATCAGGAAAGA
AGTTCGCCTGTGTGCCATTTGAAGCTGGGCATCTTCGTTGTACCGGGGAGAATTGTGCTCATGTTCAGATCAAGACAATT
GGGTCCACCACACTTTGTTGTATGAATTTGATCTCATTGATGGATATTTTCCCACTGCGATTTATACAACCATGATCCAC
ACCCCCTGAAAATTCAGTTTTCCGATACAAATGCAGATCAGAG

Alignment

ORF - retro_amel_1512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.87 %
• Parental protein coverage: 93.31 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  LLIACAFTLGLVYLFRLAVGHLAP-LPAGAKSPPYI-FSPVPFLGHAIAF-GKSPIEFLENAYEKYGPVF
          LL.A.A.TLGLVYL...AVGHLAP.LP...KSP.YI..SP.PFL..AIAF.GK......E...EKYGPVF
Retrocopy LLMA*ASTLGLVYLLCPAVGHLAP<LPTAEKSPVYI<YSPTPFLRQAIAF>GKVQLNS*E-MHEKYGPVF

Parental  SFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYGRLTTPVFGKGVAYDVPNP-VFLEQKKMLKTGLNI
          SFTMV.KTFT.L.GSDAAAL..N.KNEDLNA.DVY...T.PVFGKGVA.DV.NP.VFLEQKKMLK.GL..
Retrocopy SFTMVSKTFTHLPGSDAAALFLNGKNEDLNADDVYSHPTRPVFGKGVAQDVSNP>VFLEQKKMLKSGLYL

Parental  AHFRQHVSIIEKETKEYFQSWGESGEKNLFEALSELIILTASHC-LHGKEIRSQLNEKVAQLYADLDGGF
          AH.RQHVSI.EKETKEYF.SWG.S.EKN.FEAL.EL.ILTASHC.L.GKEIRSQL.E......ADLDGGF
Retrocopy AHIRQHVSISEKETKEYFPSWG*SREKNWFEALPELTILTASHC<LSGKEIRSQLSERHNS--ADLDGGF

Parental  SHAA-WLLPGWLPLPSFRRRDRAHREIKNIFYKAIQKRRQSEEKIDDILQTLLDSTYKDGRPLTDDEVAG
          S.AA.WL.PGWLPLPSFR.RDRAH.EIKNIF.KAIQK.R.S.E.IDD.LQT.L.STYKDG.PLTDDEVAG
Retrocopy SLAA<WLVPGWLPLPSFRYRDRAH*EIKNIFCKAIQKHRESVENIDDTLQTFLASTYKDGHPLTDDEVAG

Parental  MLIG-LLLAGQHTSSTTS-AWMGFFLARDKTLQEKCYLEQKTVCGEDLPPLTFDQLKDLNLLDRCIKETL
          ML.G.LL......S.T....W..F......T...K.....KTVC.EDLPPL..DQLKD.N.LD.CIKETL
Retrocopy MLTGPLLAG*HTSSTTGT>GWASFW---PETKRFKKNVT*KTVC-EDLPPLIYDQLKDRNFLDHCIKETL

Parental  RLRPPIMTMMRMAKTPQTVAGYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPDRYLQDNPASGEKFAYVP
          RL..P.MTMMRMAKTPQTV..YTIPPG.QVC..P.V.QRLK.SWVERLDFNPD.YLQD.PASG.KFA.VP
Retrocopy RL*LPMMTMMRMAKTPQTVTDYTIPPGQQVCAPPPVSQRLKHSWVERLDFNPDCYLQDSPASGKKFACVP

Parental  FGAGRHRCIGENFAYVQIKTIWSTML-RLYEFDLIDGYFPTVNYTTMIHT-PENPVIRYKRRSK
          F.AG..RC.GEN.A.VQIKTI.ST.L..LYEFDLIDGYFPT..YTTMIHT.PEN.V.RYK.RS.
Retrocopy FEAGHLRCTGENCAHVQIKTIGSTTL<LLYEFDLIDGYFPTAIYTTMIHT>PENSVFRYKCRSE

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_1512 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1512 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005722	1 retrocopy	retro_amel_1512 ,
Homo sapiens	ENSG00000001630	2 retrocopies	retro_hsap_1248, retro_hsap_2807,
Loxodonta africana	ENSLAFG00000000066	1 retrocopy	retro_lafr_272,
Monodelphis domestica	ENSMODG00000010610	1 retrocopy	retro_mdom_436,
Pongo abelii	ENSPPYG00000017824	2 retrocopies	retro_pabe_1039, retro_pabe_1040,
Pan troglodytes	ENSPTRG00000019391	2 retrocopies	retro_ptro_1901, retro_ptro_859,
Tarsius syrichta	ENSTSYG00000014341	1 retrocopy	retro_tsyr_1008,