RetrogeneDB ID: retro_amel_1482

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193477.1:60926..61485(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLB
• Ensembl ID: ENSAMEG00000005134
• Aliases: None
• Description: polymerase (DNA directed), beta [Source:HGNC Symbol;Acc:9174]

Sequence

>retro_amel_1482
AGCAGGTGAAAGGCACAGCCAGAGACGCTCAACAGGAAAATCACCGACATGCTCACAGAACTTGCGAACTTTGAGAAGAA
CACGAACTAGGCCATCCATAAGGACCATGCTTATAGAAAAGCAGCATCTGTGATAGCAAAGCACCCATACAAAATAAAAA
GTGGAGAAGCTAAGACATTGCCTGGAGTAGGAACAAAAATTGCTGAAAAGATTGATGAATTTTTAGGGACTGGAAAATTG
TGTAAGCTGGGAAAGATGCAGCAGGATGATACGCGTTCATCTATCAATTTCCTGACTCGAGTCCGTGGCATTGGTCCATC
TGCTGCAAGGAAGTTTATAGATGCAGGAATTAAAACATGAGAAGATCTCAGGAAAAAATGAAGGTAATAAGTTGAACCAT
CATCAGTGAATTGGGCTGAAATATTTTGAGGAATTTGAGAAAAGAATTCATCCTGAAGAAGTGTGACAAATGTAAGCCAT
TGTACTAATTGAAGTTTAAAAACTGGATTCTGAATTCCTGGCTATAGTCTGTGGTGGGTTTCACAGAGCTACAGAGTCC

Alignment

ORF - retro_amel_1482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.06 %
• Parental protein coverage: 55.52 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKRKAPQETLNGGITDMLTELANFEKNVNQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAE
          S..KA..ETLN..ITDMLTELANFEKN.N.AIHK..AYRKAASVIAK.P.KIKSG.EAK.LPGVGTKIAE
Retrocopy SR*KAQPETLNRKITDMLTELANFEKNTN*AIHKDHAYRKAASVIAKHPYKIKSG-EAKTLPGVGTKIAE

Parental  KIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLR-KNE-DKLNHHQRIG
          KIDEFL.TGKL.KL.K..QDDT.SSINFLTRV.GIGPSAARKF.D.GIKT.EDLR.KNE..KLNHHQ.IG
Retrocopy KIDEFLGTGKLCKLGKMQQDDTRSSINFLTRVRGIGPSAARKFIDAGIKT*EDLR>KNEGNKLNHHQ*IG

Parental  LKYFEDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAES
          LKYFE.FEKRI..EE..QM..IVL.EV.K.DSE..A.VCG.F.R..ES
Retrocopy LKYFEEFEKRIHPEEV*QM*AIVLIEV*KLDSEFLAIVCGGFHRATES

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_1482 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1482 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005134	1 retrocopy	retro_amel_1482 ,
Canis familiaris	ENSCAFG00000005517	1 retrocopy	retro_cfam_891,
Echinops telfairi	ENSETEG00000002644	1 retrocopy	retro_etel_37,
Macropus eugenii	ENSMEUG00000012619	1 retrocopy	retro_meug_1007,
Procavia capensis	ENSPCAG00000007734	1 retrocopy	retro_pcap_463,