RetrogeneDB ID: retro_amel_1353

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193241.1:228076..228611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2C
• Ensembl ID: ENSAMEG00000012547
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]

Sequence

>retro_amel_1353
ATGGCTTCCTAGAATTTCGACCCAGTCTCCACCAGCATTGCCACCACCCGCAAAGGAGCCAAGGCCAGCCAGAGCACTGC
CCACTCCTTGGGCAAGAGGCTACAGCAGGAGTGGATGATGCCTGGTAACAAAGGAATTTCTGTCTTCCCTGAACCAGGCA
ACCTTTTCAAATGGATAGGGACCATCCATGGAGCAGCCGGCACAGTATATGAAGATCTGAGGTATAAGCGCTCCCAGGAG
TTCCCCAGTGGCTACGCTTAAAACACATCCACGGTGCAATTACTCACACCCCGCTACCACCCCAACATGCACACCCAGGG
TGACATCTGCCTGGACATCCTGGAGGACAAGTGGTCCACCCTGTATAATTGTCAGGACCATCCTGCTGTCCATCCAGAGC
CTGCTAGGAGAACCCAACATTCACAGCCCTTTGAACACACATGCTGCTGAGCTCTTGAAAAAAAAAAAACAACCCACAAC
CTTTAAAAAGTATCTGCAAGAAACCAACTCAAAACAGGTCTCCAGCCAAGAACCC

Alignment

ORF - retro_amel_1353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASQNRDPAAASVAAARKGAEPSGGAARGPVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA
          MAS.N.DP...S.A..RKGA..S...A....GKRLQQE....MM.G.KGIS.FPE..NLFKW.GTIHGAA
Retrocopy MAS*NFDPVSTSIATTRKGAKASQSTAHS-LGKRLQQEW---MMPGNKGISVFPEPGNLFKWIGTIHGAA

Parental  GTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKDKWSALYD-VRTILLSIQSLL
          GTVYEDLRYK.S.EFPSGY..N..TV..LTP.YHPN..TQG.ICLDIL.DKWS.LY..VRTILLSIQSLL
Retrocopy GTVYEDLRYKRSQEFPSGYA*NTSTVQLLTPRYHPNMHTQGDICLDILEDKWSTLYN>VRTILLSIQSLL

Parental  GAIEPNIDSPLNTHAAEL---WKNPTAFKKYVQETYSKQLSSQDP
          G..EPNI.SPLNTHAAEL......PT.FKKY.QET.SKQ.SSQ.P
Retrocopy G--EPNIHSPLNTHAAELLXXXXQPTTFKKYLQETNSKQVSSQEP

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_1353 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1353 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 8 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012547	5 retrocopies	retro_amel_1122, retro_amel_1353 , retro_amel_157, retro_amel_1621, retro_amel_635,
Loxodonta africana	ENSLAFG00000003164	1 retrocopy	retro_lafr_73,
Macropus eugenii	ENSMEUG00000007177	14 retrocopies	retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Macaca mulatta	ENSMMUG00000021023	4 retrocopies	retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica	ENSMODG00000013661	6 retrocopies	retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mustela putorius furo	ENSMPUG00000017619	2 retrocopies	retro_mputfur_103, retro_mputfur_189,
Otolemur garnettii	ENSOGAG00000004989	3 retrocopies	retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Pan troglodytes	ENSPTRG00000013564	1 retrocopy	retro_ptro_38,