RetrogeneDB ID: retro_amel_828

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192666.1:644662..645526(-)
• Located in intron of: ENSAMEG00000011127

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSAMEG00000015405
• Aliases: None
• Description: t-complex 1 [Source:HGNC Symbol;Acc:11655]

Sequence

>retro_amel_828
ATAGAGGGGCCTTTGTCTGTGTTCGGAGAATATCCCTGGGGAGCGATCCGCTCCCAGAACGTTATGGCTGTGGCTTCCAT
TGCCAGTATCGTAAAAAGGTGTCTTGGTGCAGTTGCTTGGGTGAAATGTTGGTGGATGATATTGGTGATGTAACCATTAC
TAATGACGGTGCAACCATCCTGAAGTTATTGCAGGTTAGAATATCCTGCAGCTCAAGTTCTTTGTGAGCTAGCTGATCTG
CGAGACAAAGAAGTGGGAGATGGAATCACCTCAGTGGTTATTATTGCAGCAGAACTTCTTAAAAATGCAAATGAACTAGT
GAAACAGAAAATTCATCCCACATCAGTTATTAGTAGCTATCGACTTGCTTGCAAGGAGGCAGTGCGTTACATCAGTGAAA
ATCTAATTATTAACACAGATGAACTTGGAAGAGATTACCTGATCAATGCTGCTAAGACACCTATGTCTTCCAAAATCATT
GGAATAAATGGTGATTTCTTTGCCAATATGGTAGTAGATGCTGTACTTGCAGTTAAATACACAGATGTAAGAGGCCAGCC
TTGCTAGCCAGTCAATTCCATTAATATTCTGAAAGCCCATGGGAGCAGTCAGATGGCGAATATGCTCAGCGGCTATGCAC
TCAACTGTGTGGTGAGATCCCAGGGCATGCCCAAGAGAATAGTTAATGCAAAAATTGCTTGCCTTGACTTCAGCCTGCAG
AAAACAAAAATGAAGCTTGGTGTACAGGCGGCTATTACAGACCCTGAGAAACTGGACCAGATTAGACAGAGAGAATCCGA
TATCAGCAAGGAGCGGATCCAGAAGATCCTGGCTACCGGTACGAACGTTACTCTAACCACTGGT

Alignment

ORF - retro_amel_828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.32 %
• Parental protein coverage: 52.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGPLSVFGDRSTGEAIRTQNAFMAAASIANIVKSSLGPVG-LDKMLVDDIGDVTITNDGATILKLLEV-
          .EGPLSVFG....G.AIR.QN..MA.ASIA.IVK..LG.V..L..MLVDDIGDVTITNDGATILKLL.V.
Retrocopy IEGPLSVFGEYPWG-AIRSQNV-MAVASIASIVKRCLGAVA<LGEMLVDDIGDVTITNDGATILKLLQV>

Parental  EHPAAKVLCELADLQDKEVGDGTTSVVIIAAELLKNADELVKQKIHPTSVISGYRLACKEAVRYISENLI
          E.PAA.VLCELADL.DKEVGDG.TSVVIIAAELLKNA.ELVKQKIHPTSVIS.YRLACKEAVRYISENLI
Retrocopy EYPAAQVLCELADLRDKEVGDGITSVVIIAAELLKNANELVKQKIHPTSVISSYRLACKEAVRYISENLI

Parental  INTDELGRDCLINAAKTSMSSKIIGINGDFFANMVVDAVLAVKYTDVRGQPRYPVNSINILKAHGRSQTE
          INTDELGRD.LINAAKT.MSSKIIGINGDFFANMVVDAVLAVKYTDVRGQP..PVNSINILKAHG.SQ..
Retrocopy INTDELGRDYLINAAKTPMSSKIIGINGDFFANMVVDAVLAVKYTDVRGQPC*PVNSINILKAHGSSQMA

Parental  SMLISGYALNCVVGSQGMTKRIVNAKIACLDFSLQKAKMKLGVQVVITDPEKLDQIRQRESDITKERIQK
          .ML.SGYALNCVV.SQGM.KRIVNAKIACLDFSLQK.KMKLGVQ..ITDPEKLDQIRQRESDI.KERIQK
Retrocopy NML-SGYALNCVVRSQGMPKRIVNAKIACLDFSLQKTKMKLGVQAAITDPEKLDQIRQRESDISKERIQK

Parental  ILATGANVILTTG
          ILATG.NV.LTTG
Retrocopy ILATGTNVTLTTG

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_828 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_828 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 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828 ,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Rattus norvegicus	ENSRNOG00000014160	1 retrocopy	retro_rnor_2091,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,