RetrogeneDB ID: retro_amel_960

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192769.1:85483..86054(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNG2
• Ensembl ID: ENSAMEG00000013793
• Aliases: None
• Description: cyclin G2 [Source:HGNC Symbol;Acc:1593]

Sequence

>retro_amel_960
ACTCATGAAGTAATCCAGATTAGTCGATGTAAATGCACTGCTTCTGACAGAAAATGAAGGGAAAATATACTTTTGGGAAA
AAATTCAGAACTATGAAATGGAACATGATGCTGTCTTAAACTTCTTTCTACTTATATAAGGCTGTTGTACTTCATATTCC
AGAAAGAAAGAAATATTGAGGCTTAGTAATCTGGTAGCTCAGCTGAAAGCTTGCAGTTTTCAACTAGTCTTTTCAAAAGC
AAAGCCCTCTGCATTAGCTTTGTGCCTTCTCAGTCTGGAAGCACAAACATAATTCATTAAATTATCACAAGTTCTCCTGC
TTGTGATAAAGCATTTGAAGATTAATGACGCTGAGTTCTTTTGTTGGAGGGAGGTAATTTCTAAATGTCCAGCTGACTAG
TTTCTCTCGAACGTTGCAAGAAGTTGGTTTGGATTGTTTCTAGGTGCAGAGCCCAGTCCTCCAAGACAGCAACTGTGGTG
TTTCTGAGTTGTAAACAATACCAGCGGATAGAGCCTTGATGAAAGTGAGGACTCTGAAGAGGTGAATTCTAAAGAATGAA
GTCTCAGCAGC

Alignment

ORF - retro_amel_960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.59 %
• Parental protein coverage: 57.73 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  THDVIRISQCKCTASDIKRMEKIIS-EKL-HYELEATTALNFL-HLYHTIVLYHTSERK-EILSLDKLEA
          TH.VI.IS.CKCTASD.K..E.I...EK...YE.E....LNF...LY...VL.H..ERK.EIL.L..L.A
Retrocopy THEVIQISRCKCTASDRK*RENILL>EKIQNYEMEHDAVLNFF>YLYKAVVL-HIPERK<EILRLSNLVA

Parental  QLKACNCRLIFSKAKPSVLALCLLNLEVETLKSIELLEILLLVKKHSKVNDTEFIYWRELVSKCLAE-YS
          QLKAC...L.FSKAKPS.LALCLL.LE..T...I.L...LLLV.KH.K.ND.EF..WRE..SKC.A....
Retrocopy QLKACSFQLVFSKAKPSALALCLLSLEAQT-*FIKLSQVLLLVIKHLKINDAEFFCWREVISKCPAD<LV

Parental  SPECCKPDLKKLVWIVSRRTAQN-LHNSYYSVPELPTIP-EGGCFDESESEDSCEDMSCEDSLSS
          S.E.CK....KLVWIVSR..AQ..L..S...V.EL.TIP..G...DE..SEDS.E..S.E.SLSS
Retrocopy SLERCK----KLVWIVSRCRAQS<LQDSNCGVSEL*TIP<SG*SLDE--SEDSEEVNSKE*SLSS

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_960 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_960 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 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013793	1 retrocopy	retro_amel_960 ,
Dasypus novemcinctus	ENSDNOG00000005210	1 retrocopy	retro_dnov_2498,
Felis catus	ENSFCAG00000026008	1 retrocopy	retro_fcat_1062,
Macropus eugenii	ENSMEUG00000008707	1 retrocopy	retro_meug_1962,
Macaca mulatta	ENSMMUG00000000914	1 retrocopy	retro_mmul_879,
Monodelphis domestica	ENSMODG00000011779	1 retrocopy	retro_mdom_358,
Nomascus leucogenys	ENSNLEG00000008169	1 retrocopy	retro_nleu_933,
Pongo abelii	ENSPPYG00000014867	1 retrocopy	retro_pabe_942,
Pan troglodytes	ENSPTRG00000016196	1 retrocopy	retro_ptro_773,
Sus scrofa	ENSSSCG00000008988	1 retrocopy	retro_sscr_813,
Ictidomys tridecemlineatus	ENSSTOG00000027922	1 retrocopy	retro_itri_1112,
Tupaia belangeri	ENSTBEG00000007671	2 retrocopies	retro_tbel_2258, retro_tbel_38,
Tursiops truncatus	ENSTTRG00000014837	1 retrocopy	retro_ttru_491,