RetrogeneDB ID: retro_amel_370

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192409.1:1786636..1787276(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSAMEG00000003535
• Aliases: None
• Description: general transcription factor IIIC, polypeptide 6, alpha 35kDa [Source:HGNC Symbol;Acc:20872]

Sequence

>retro_amel_370
GGAATCATGGCAGCAACTGAGAGTGGACCCAGGAGGACGAGCGAGAGGAAGAAGAGGAACTGGAGCGGTTGGTTTTGTGG
AATTGTCCAGGATTATTGATTCAGACTTTCTATCAAACGGGGAAAATAAATGCAAACTTGGGGAATTGACACGGAGAGGC
CCATTCCACAAGTGGGCAGCTACGTCCTTGCTGGAGAGCGTGAAGATGCTCTTGGGACCTGTGTTACATTTGAAGCAAAT
GTTGAACATGGTGATGCAGAGGGCAGTAATAAAACAGTGCTGAGCTATACATGCCATACAATGAAGAAGTTCAGTATGAC
AAGAACTCTTTCGACAGCAAAGAAGGAAGGAGAAGAAAGCACAGGTGGTATGGAATGGCTGCAAATCAAAGACAATGATT
TCTCCTATAGACCCAACATGATTTGTATCTTTCTGCATGAAAATGAAGATGACAGCGTTGTAGCTCCAGCCTCAGATAAA
TCTTCGGAGTTGGAAGAGCAAGAGATTCAAAGGCAAGACAATTCAAACCTGAGTTATGAACAGGGGAAATCACTGAACTT
GGAAGTAGAGAATTCTGGTTCTCTTATTGATATTCCTCCTTCCGAGATGGAAGTTTATGTCCTTTATGGAAACTCAAGAT

Alignment

ORF - retro_amel_370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GIMAATE-ERIREDGEEEEEEAQEQLVL-VELSGIIDSDFLSKCENKCKI-LGIDTERPILQVDNYVFAG
          GIMAATE.E...ED..EEEEE..E.LVL.VELS.IIDSDFLS..ENKCK...GIDTERPI.QV..YV.AG
Retrocopy GIMAATE<EWTQEDEREEEEEL-ERLVL<VELSRIIDSDFLSNGENKCKL<WGIDTERPIPQVGSYVLAG

Parental  EYEDTLGTCAIFEENVEHGDTEGSNKTVLKYTCHTMKKLSMTRTLLTEKKEGEESIGGVEWLQIKDNDFS
          E.ED.LGTC..FE.NVEHGD.EGSNKTVL.YTCHTMKK.SMTRTL.T.KKEGEES.GG.EWLQIKDNDFS
Retrocopy EREDALGTCVTFEANVEHGDAEGSNKTVLSYTCHTMKKFSMTRTLSTAKKEGEESTGGMEWLQIKDNDFS

Parental  YRPNMICSFLHEHEDDDVVAPASDKSLELEEQEIQTKDNSNLSYEQGKSLNLEVENSGPLIDIPSSDTEG
          YRPNMIC.FLHE.EDD.VVAPASDKS.ELEEQEIQ..DNSNLSYEQGKSLNLEVENSG.LIDIP.S..E.
Retrocopy YRPNMICIFLHENEDDSVVAPASDKSSELEEQEIQRQDNSNLSYEQGKSLNLEVENSGSLIDIPPSEMEV

Parental  YV-FMEPQD
          YV.FME.QD
Retrocopy YV>FMETQD

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_370 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_370 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	ENSAMEG00000003535	1 retrocopy	retro_amel_370 ,
Callithrix jacchus	ENSCJAG00000005248	2 retrocopies	retro_cjac_3118, retro_cjac_4098,
Dasypus novemcinctus	ENSDNOG00000014270	4 retrocopies	retro_dnov_1228, retro_dnov_1654, retro_dnov_377, retro_dnov_931,
Homo sapiens	ENSG00000155115	3 retrocopies	retro_hsap_3714, retro_hsap_4728, retro_hsap_4735,
Gorilla gorilla	ENSGGOG00000010681	1 retrocopy	retro_ggor_2511,
Myotis lucifugus	ENSMLUG00000013919	1 retrocopy	retro_mluc_897,
Macaca mulatta	ENSMMUG00000012709	3 retrocopies	retro_mmul_1700, retro_mmul_2520, retro_mmul_2524,
Monodelphis domestica	ENSMODG00000017924	1 retrocopy	retro_mdom_876,
Mustela putorius furo	ENSMPUG00000010179	1 retrocopy	retro_mputfur_182,
Nomascus leucogenys	ENSNLEG00000012846	3 retrocopies	retro_nleu_1237, retro_nleu_2122, retro_nleu_2552,
Pan troglodytes	ENSPTRG00000018502	3 retrocopies	retro_ptro_2516, retro_ptro_3145, retro_ptro_3149,