RetrogeneDB ID: retro_amel_1403

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193329.1:151453..152111(-)
• Located in intron of: ENSAMEG00000017115

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPB
• Ensembl ID: ENSAMEG00000011353
• Aliases: None
• Description: Small nuclear ribonucleoprotein-associated protein [Source:UniProtKB/TrEMBL;Acc:G1LXZ2]

Sequence

>retro_amel_1403
GGCCAGAGCAGCAAGATGCTGCAGACTTGAATTACAGGGTGAGGGGCATCCTGCAGGACAGCCCTATCTTCCCTGGCACC
TCCAGGGTTTCAACAAACATAGGAATTTGAAACTCTGTGACTATAATGAGTTCAAGACAAAGAACTCAAAACAACAGAAA
GGGAAGAGACCGAAGCACAGGTCTGGTGCTGCAGGTCTGGTAGGTCCTGGTCTTAATGACAGCAGAAGAACCTCCACTCA
AAGATAAAGACATTGCCTGAGTGCCCTTTGAGAGCAGCCAGGAGTCCAGGGATTGGTAGAGCTGCTGGCAGAGGAATCCC
AGTTGGTGTTCCGATGCCCCAGGCTCCTGCAGGACTCACTGGGCCAGTCCCAAGGGGTGGTGTGTTACTGCAGCAGGTGA
TAACCCTGCAAGGAAGAGGCCTGTTTACAGCTGCTGCCATTGCTGCTGCAGCCAGGATTTCAGGGACCCCAACCCAATAT
CAAACTGGCTGTGGGGATCCTCCACCATCTTATGGGTCAAGGGTCACCCACTCCAGTCATGATGGGCCCAGCACCTGGTG
TGAGGCCTCCCATGGGTCCCCCAGTGGGGATCGCCACTGGATGAGGAACTCCAATGCACATGCCCACTTTAGGAAGTGGC
CCCCTCCCCAGGGGGATG

Alignment

ORF - retro_amel_1403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.17 %
• Parental protein coverage: 92.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GKSSKMLQ-HIDYRMRCILQDGRIFIGT-FKAFDKHMNLILCDCDEFRKIKPKNSKQ-AEREEK-RVLGL
          G.SSKMLQ....YR.R.ILQD..IF.GT....F.KH.NL.LCD..EF...K.KNSKQ..EREE..R..GL
Retrocopy GQSSKMLQ<DLNYRVRGILQDSPIFPGT<LQGFNKHRNLKLCDYNEF---KTKNSKQ<TEREET<RSTGL

Parental  VLLRGENLVSMTVEGPPPKDTGIARV-PLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPS
          VL.....LV.MT.E.PP.KD..IA.V.PL..AA..PGIGRAAGRGIP.GVPMPQAPAGL.GPV...G...
Retrocopy VLQVW*VLVLMTAEEPPLKDKDIA*V>PLR-AARSPGIGRAAGRGIPVGVPMPQAPAGLTGPVPRGGVLL

Parental  QQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPP-MGRGAPPPGMMGPPPGMRPPMGPPMGIPP
          QQV.T.QGRG...AAA.AA.A.I.G.PTQY..G.G.PPP..MG.G.P.P.MMGP.PG.RPPMGPP.GI..
Retrocopy QQVITLQGRGLFTAAAIAAAARISGTPTQYQTGCGDPPPS>MGQGSPTPVMMGPAPGVRPPMGPPVGIAT

Parental  GRGTPMGMPPPGMRPPPPGM
          G.GTPM.MP..G..P.P.GM
Retrocopy G*GTPMHMPTLGSGPLPRGM

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_1403 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1403 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 17 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007034	3 retrocopies	retro_amel_1048, retro_amel_714, retro_amel_839,
Ailuropoda melanoleuca	ENSAMEG00000011353	1 retrocopy	retro_amel_1403 ,
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Dasypus novemcinctus	ENSDNOG00000007896	2 retrocopies	retro_dnov_2060, retro_dnov_2471,
Erinaceus europaeus	ENSEEUG00000015568	3 retrocopies	retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus	ENSFCAG00000014447	2 retrocopies	retro_fcat_1788, retro_fcat_1960,
Microcebus murinus	ENSMICG00000016519	4 retrocopies	retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861,
Myotis lucifugus	ENSMLUG00000016951	1 retrocopy	retro_mluc_1725,
Mustela putorius furo	ENSMPUG00000009283	1 retrocopy	retro_mputfur_1153,
Nomascus leucogenys	ENSNLEG00000009206	1 retrocopy	retro_nleu_761,
Otolemur garnettii	ENSOGAG00000016149	4 retrocopies	retro_ogar_2197, retro_ogar_2841, retro_ogar_2918, retro_ogar_3236,
Ochotona princeps	ENSOPRG00000007459	2 retrocopies	retro_opri_697, retro_opri_72,
Pongo abelii	ENSPPYG00000010841	1 retrocopy	retro_pabe_2265,
Pteropus vampyrus	ENSPVAG00000017013	1 retrocopy	retro_pvam_289,
Tupaia belangeri	ENSTBEG00000010040	3 retrocopies	retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta	ENSTSYG00000014498	2 retrocopies	retro_tsyr_45, retro_tsyr_719,