RetrogeneDB ID: retro_amel_102

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194087.1:300415..301162(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019145
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FAM133B
• Ensembl ID: ENSAMEG00000007438
• Aliases: None
• Description: None

Sequence

>retro_amel_102
ATGGGGAAGCGGGATAATCGAGTGGCCTACATGAATCCTATAGCAATGGCCAGATGGAGGGGCCCAACTCAATCTACAGG
CCCAACAATACAAGATTATCTGAATCGACCAAGGCCTACCTGGGAAGAAGTGAAGAAACAATTAGAAAATAAAAAGAAAG
GCTCCAAGGCATTAGCTGAATTTGAAGAAAAAATGAATGAGAATTGGAAAAAAGAATTAGAAAAAAGTAGGGAGAAATTA
TTGAGTGGAAATGAGAGCTCTTCTAAAAAAAAAGAAAAAAAGAAAAAGAAAAAGAAGAAATCTTGTCCAAGGTCTTCATC
TTCTTCTTCATCAATTTCTGATTCTTCAAGCAGTTCAGATTCTGAGAATGAGGAAAAGAAACAAGGAAAAAAGAGAAAGA
AAAAGAAGAACCATTCATACAAATCATCAGAAAGGTCTACATATGAATCTGAATCAGAAAGCAAGGAATCTGTGAAAAAG
AAAAAGAAGTCAAAAGATGAAACAGAGAAAGAAAAGTATATTAGAAGTCTCAGCAAAAAAAGAAAGAAGACTTATCCTGA
AGATAAACCCTCATCATCAGAGTCCTCATCAGAATCAGATTATGAAGAGGAAGTGCAAGCAAAAAAGAAGAGAAGACATG
AAGAGCAAGAAAAAGCAACAGAAAAAGCAAAGAAAAAGAAGAAGAAACAGCGCAAGAAACATAGTAAGAAGAAAAAGAAG
TCGGGTTCAAGTCACAAGTCAGGATAA

Alignment

ORF - retro_amel_102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.41 %
• Parental protein coverage: 97.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
          MGKRDNRVAYMNPIAMAR.RGP.QS.GPTIQDYLNRPRPTWEEVK.QLE.KKKGSKALAEFEEKMNENWK
Retrocopy MGKRDNRVAYMNPIAMARWRGPTQSTGPTIQDYLNRPRPTWEEVKKQLENKKKGSKALAEFEEKMNENWK

Parental  KELEKHREKLLSGSESSSKKRQSQAFIVLCLVKYSSSSSSSSDSSSSSSDSEDEDKKQGKRKKKKKNRSH
          KELEK.REKLLSG.ESSSKK..............SSSSSSS...SSSSSDSE.E.KKQGK..KKKKN.S.
Retrocopy KELEKSREKLLSGNESSSKKKEKKKKKKKKSCPRSSSSSSSISDSSSSSDSENEEKKQGKKRKKKKNHSY

Parental  KSSESSMSETESDSKDSLKKKKKSKDATEKEKDIKGLSKKR-KMYPEDKPLSSESLSESDYIEEVRAKKK
          KSSE.S..E.ES.SK.S.KKKKKSKD.TEKEK.I..LSKKR.K.YPEDKP.SSES.SESDY.EEV.AKKK
Retrocopy KSSERSTYESESESKESVKKKKKSKDETEKEKYIRSLSKKRKKTYPEDKPSSSESSSESDYEEEVQAKKK

Parental  KSSEEREKVIEKTKKKKK--HKKHSKKKKKKATS
          ...EE.EK..EK.KKKKK...KKHSKKKKK...S
Retrocopy RRHEEQEKATEKAKKKKKKQRKKHSKKKKKSGSS

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_102 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_102 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 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102 ,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,