RetrogeneDB ID: retro_amel_627

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192534.1:403479..404202(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLZF1
• Ensembl ID: ENSAMEG00000011473
• Aliases: None
• Description: basic leucine zipper nuclear factor 1 [Source:HGNC Symbol;Acc:1065]

Sequence

>retro_amel_627
ACAGAGGTCAATTGTGAGTTTAAAAGATTGCCAGGGGCTTCTGCTGGGGATGATCTTCAGTATCACTTTGAATGTCTAGC
CCCTGAGAAAAATTGGCTTATTTTAGAAAATGAAGCCCTAGGTCAAAACACAGCTCAACTTTCTGAATAGTTAGAACATA
TGTCAATGTAGTGTGCTGTATGGCAAAGTAAATTCCTCACAAGCAGGATTATAGCAGATGAGTTAACCAACTCTAGACCA
GGTTCATAGCATCAAAATCTTGATGCACAGAGTGCTATTCAAAATCTCCTGAGTGAATGGGAATAGTTTCATTAGGAAAT
GACAGTTACCCAGAAACTGTCAGAGGAGCGCTTAATCTCCTTGCAGTGGGAAGAGAGCACACTTGCTACCCTAGTACAGA
GCCTCACACCAAAGCAGTACTAGCATAACAAATGAAGTTGGCAAAAGCAGTAAATGTGTGTCTTCTGGATAACGCTGACG
CTAAAAGTCAAAAGAAGATTCCATCAACAGTTGAATTTTGTAGCACCCAGCAGAAAAAAATGGCTGGAAGGGTTCTACTC
ATTTTGGATCCAGTTATCTATACAGAAAGCTCACTTGATAATCCATTTTCTAAGCCTTCACCTTACTTGCTACAAAGAAA
AATATTGGATAATTTCATCCCTATACAGATATGAAAGTACAACTTTGAGTTGTTGCAATCACTGCAAGGGAGAGCTCGTT
GTC

Alignment

ORF - retro_amel_627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.94 %
• Parental protein coverage: 60.34 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TEVNRELKKLLVASVGDDLQYHFERLAREKNQLILENEALGQNTAQLSEQLERMSIQCDVWRSKFLASRV
          TEVN.E.K.L..AS.GDDLQYHFE.LA.EKN.LILENEALGQNTAQLSE.LE.MS..C.VW.SKFL.SR.
Retrocopy TEVNCEFKRLPGASAGDDLQYHFECLAPEKNWLILENEALGQNTAQLSE*LEHMSM*CAVWQSKFLTSRI

Parental  MADELTNSRAGLQRQNRDAQSAIQDLLSEREQFRQEMIATQKLLEELLVSLQW-GREQTYYPSAQPHTTA
          .ADELTNSR.G...QN.DAQSAIQ.LLSE.E.F..EM..TQKL.EE.L.SLQW.GRE.T.YPS..PHT.A
Retrocopy IADELTNSRPGS*HQNLDAQSAIQNLLSEWE*FH*EMTVTQKLSEERLISLQW<GREHTCYPSTEPHTKA

Parental  ELALTNHKLAKAINAHLLGNVGANSQKKIPSTVEFCSTPAEKMAETVLRILDPVTCTESSPNTPFSESSP
          .LA....KLAKA.N..LL.N..A.SQKKIPSTVEFCST...KMA..VL.ILDPV..TESS...PFS..SP
Retrocopy VLA-*QMKLAKAVNVCLLDNADAKSQKKIPSTVEFCSTQQKKMAGRVLLILDPVIYTESSLDNPFSKPSP

Parental  TALLATKKNIGRF-HPYT-RYENITFNCCNHCRGELIV
          ...L...K....F.HPYT.RYE..T..CCNHC.GEL.V
Retrocopy --YLLQRKILDNF<HPYT<RYESTTLSCCNHCKGELVV

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_627 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_627 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011473	1 retrocopy	retro_amel_627 ,
Choloepus hoffmanni	ENSCHOG00000008235	1 retrocopy	retro_chof_1515,
Echinops telfairi	ENSETEG00000008147	1 retrocopy	retro_etel_53,
Tupaia belangeri	ENSTBEG00000003379	1 retrocopy	retro_tbel_2191,