RetrogeneDB ID: retro_amel_1104

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192907.1:857984..858469(+)
• Located in intron of: ENSAMEG00000008861

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC3
• Ensembl ID: ENSAMEG00000017364
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3) [Source:HGNC Symbol;Acc:9803]

Sequence

>retro_amel_1104
TTCTCTAGAGAATACAGCCCCACTGTCTTTGACAACTACTCTGCCAATGTTATGGTAGGTGGAAAACGGGTGAATCTGGG
CTTATGGGATACAGCTGGACAAGAAGATTATGACAGATTACATCCCTTATCCTATCCACAAACAGATATGGTCATAATTT
GCTTTTCTCTCCTGAGTCCTTCATCATTTGAAAATGTTCGAGCACGGTGGTACCTGAAGTGCGACACCACTGTCCCAACA
CCCCTATCATCCTGGTGGAGACTAAACTTGATCTCAGGGACAACAAAGATGTGATTGAGCAACTGCTGGAGAAGCTGACT
CCCATCACCAGCCGCAGGGTTTGGCCAGGGCTAAGGAGATCAGTGCTGGAAAGCACCTGAGTGCTCGGCTCTCCTGCAGC
GAGGCCTCCAGACAGAGTGGGATGAAGCTCTTCGAGGATTCTCTGCCCTCCACCGGTCAAGAAGAGGAAGAGAAAATGCT
TCATT

Alignment

ORF - retro_amel_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.21 %
• Parental protein coverage: 86.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKW
          F..EY.PTVFDNYSANVMV.GK.VNLGLWDTAGQEDYDRL.PLSYPQTD...ICFSL.SP.SFENVRA.W
Retrocopy FSREYSPTVFDNYSANVMVGGKRVNLGLWDTAGQEDYDRLHPLSYPQTDMVIICFSLLSPSSFENVRARW

Parental  Y-PEVRHHCPHTPILLVGTKLDLRDDKDTIERLRDKKLAPIT-YPQGLAMAREIGSVKYL-ECSALTQRG
          Y.PEVRHHCP.TPI.LV.TKLDLRD.KD.IE.L...KL.PIT..PQGLA.A.EI...K.L.ECSAL.QRG
Retrocopy Y<PEVRHHCPNTPIILVETKLDLRDNKDVIEQLLE-KLTPIT<QPQGLARAKEISAGKHL<ECSALLQRG

Parental  LKTVFDEAIRA-VLCPPPVKKPGKKCTV
          L.T..DEA.R...LCPPPVKK...KC..
Retrocopy LQTEWDEALRG<ILCPPPVKKRKRKCFI

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_1104 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1104 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006082	1 retrocopy	retro_amel_383,
Ailuropoda melanoleuca	ENSAMEG00000009889	2 retrocopies	retro_amel_1691, retro_amel_647,
Ailuropoda melanoleuca	ENSAMEG00000017364	1 retrocopy	retro_amel_1104 ,
Callithrix jacchus	ENSCJAG00000018194	1 retrocopy	retro_cjac_2687,
Cavia porcellus	ENSCPOG00000013861	1 retrocopy	retro_cpor_18,
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Macropus eugenii	ENSMEUG00000006196	1 retrocopy	retro_meug_201,
Otolemur garnettii	ENSOGAG00000012467	1 retrocopy	retro_ogar_2140,
Procavia capensis	ENSPCAG00000009949	1 retrocopy	retro_pcap_16,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047, retro_pabe_2546,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15,