RetrogeneDB ID: retro_amel_483

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192470.1:774531..775079(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSAMEG00000003515
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:HGNC Symbol;Acc:12477]

Sequence

>retro_amel_483
TCGAGGGACAGCACCAGCTCCTCCTCATATTCATCCTCCAACCAGCAAACCGAGAAAGAGACGAACACCTCCAAGAAGAG
AATAAAGTCAGAATGAGCAAAAACTCCAAACCGGCATCAACAGGATTCAGAAGGAACTGACAGACATCACTGTAGACACT
CCGTCTCACTGTAGTGCTGGTCCTAAAGGTGGTAACATCTATGAATGGAGATCGACCATTCTAGGGCCTTTAAGATCCAT
GTTTGAGGGTGGTGTATTCTTCCTTAATACCACTTTTACACCAGAAGACTCCTTCAACCCTCCAAAGGTTACATTTTGGA
CAAGAATCTATCACTATAACAATAACAGTCAAGGAGTTATTTGCTTGGACATATTAAAGGAAATTGGAGTCCAACACTAA
TCATTTCTGAAGTTCTCCTCTCTATCTGCTCCCTTCTTACAGACTGTAATCCTGCTGACCGTTTGGTGGGAAGGGTTGCC
ACTGAGTGTAGGAAAACAGAGCAGAACATGACAGAATGGCCAGAAAATGGACCAAGAGATACACTTCA

Alignment

ORF - retro_amel_483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.59 %
• Parental protein coverage: 94.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SSSSSSSSNQQTEKETNTPKKKESKVSM-SKNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEW
          S..S.SSS...............SK....S.N...L.T...RIQKEL.DIT.D.P..CSAGPKG.NIYEW
Retrocopy SRDSTSSSSYSSSNQQTEKETNTSKKRI>SQNEQKLQTGINRIQKELTDITVDTPSHCSAGPKGGNIYEW

Parental  RSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKD-NWSPALTISKV
          RSTILGP..S..EGGVFFL..TFTPE..F.PPKVTF.TRIYH.N.NSQGVICLDILK..NWSP.L.IS.V
Retrocopy RSTILGPLRSMFEGGVFFLNTTFTPEDSFNPPKVTFWTRIYHYNNNSQGVICLDILKE<NWSPTLIISEV

Parental  LLSICSLLTDCNPADPLVGSIATQYM-TNRAEHDRMARQWTKRYAT
          LLSICSLLTDCNPAD.LVG..AT.....NRAEHDRMAR.WTKRY..
Retrocopy LLSICSLLTDCNPADRLVGRVATECR<ENRAEHDRMARKWTKRYTS

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_483 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_483 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003515	2 retrocopies	retro_amel_1117, retro_amel_483 ,
Ailuropoda melanoleuca	ENSAMEG00000011216	6 retrocopies	retro_amel_1295, retro_amel_1427, retro_amel_1648, retro_amel_1750, retro_amel_620, retro_amel_995,
Ailuropoda melanoleuca	ENSAMEG00000014519	1 retrocopy	retro_amel_1385,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Felis catus	ENSFCAG00000024719	1 retrocopy	retro_fcat_623,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,