RetrogeneDB ID: retro_amel_1407

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193333.1:2723..3334(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000011920
• Aliases: None
• Description: None

Sequence

>retro_amel_1407
GTCTCAAGAGAAGTTTCTCAAAGACCTGGTACCCACTGAACTGTGAAGAAGATTTGTGTTGGTGGCATTAAAGAAGACAC
TGAAGAACCTCACGTGAGAGACTATTTTGATCAGAACGGGAAAACTGACGTGGCTGAAATCATGACTGACCGAGGCAGTG
GTAAGAAGAGAGACTTTGCTTTTATAACACTTGAAGATCATGACTCTGTAGATGAGATTGTCATTAAGAAGTACCGTACT
GTGAATGGCCACATCTAAGCAGGGTGAAAGCCCTATCTAAGCAAGAGATGGCTAGTACTTCGTCCAGCCAAAGAGGTCAA
AGTGGTTTGGGAAACTTTGCTGGTGGTCGTGGAGGTAGTTTTGGTGGGAATGACAACTTTGGTCATGGAGGAAACATCGG
TGGGCGAGGTGGCTTTGGTGGCAGTCAAGGTGGTGGTGGATATGGTGGCAGCAGGGATGGCTATAACAGATTTGGTAATG
ATGGAAGCAACTTTGGAGGTGGTGGAAGTTATGATGATTTTGGCTATCAGCATAGTCAATCTGCAAATTTTGGACCCATG
AACAGAGGAAATTCTGGAGGCCGAAGCTCTGGCCCCTGTGGTGGTGGAGGC

Alignment

ORF - retro_amel_1407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.29 %
• Parental protein coverage: 56.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTV
          VSRE.S..PG.H.TVKKI.VGGIKEDTEE...RDYF...GK....E.M.DR.SGKKR.FAF.T..DHD.V
Retrocopy VSREVSQRPGTH*TVKKICVGGIKEDTEEPHVRDYFDQNGKTDVAEIMTDRGSGKKRDFAFITLEDHDSV

Parental  DKIVVQKYHTINGH-NCEVKKALSKQEMQSAGSQRGRGGGSGNFM-GRGGNFGGGGNFGRGGNFGGRGGY
          D.IV..KY.T.NGH......KALSKQEM.S..S......G.GNF..GRGG.FGG..NFG.GGN.GGRGG.
Retrocopy DEIVIKKYRTVNGH<HLSRVKALSKQEMASTSSSQRGQSGLGNFAGGRGGSFGGNDNFGHGGNIGGRGGF

Parental  GGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGCGGPGYSSRGGYGASGHQGGRYGGGG
          GG..GG..G.YGG...GYN.FG.DG.N.GGG..Y....GY.................G...G..GGGG
Retrocopy GGSQGG--GGYGGSRDGYNRFGNDGSNFGGGGSYDD-FGYQHSQSANFGPMNRGNSGGRSSGPCGGGG

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_1407 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1407 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 18 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000717	3 retrocopies	retro_amel_1726, retro_amel_547, retro_amel_925,
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407 , retro_amel_557, retro_amel_715, retro_amel_765,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Pongo abelii	ENSPPYG00000012967	1 retrocopy	retro_pabe_450,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,