RetrogeneDB ID: retro_amel_1479

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193467.1:172999..173669(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC43
• Ensembl ID: ENSAMEG00000018379
• Aliases: None
• Description: None

Sequence

>retro_amel_1479
ATGGCGGCACCCAGCGAAGTGATTGCAGCTGCCTTGGGTGAAGGCGATGGTGGAGGCAGTGGCTTTGGGTCTTGACTTGT
GGATAGACAGACGGTTCGAGGCGCTGGGAGTAGACTGAGCCATAGGGCACCTACATCTTGGTGTCCTGCAGGAGGAGGAG
GAAGAAGAGAAGCTGGACACTCTGCAGGGTATACTCTCTGCCTTCTTGGAAGAAGATTCTCTTAACATCTGCAAGGAGAT
TGTGGAACGATGGTCAGAAAGTCAGAATGTTCTCACCAAAGTGAAAAAAGAAGATGAGATAGAGGTCATTGCCACCTAAA
TTTAGAAGCAGGGACAGATTGTGGTGAAGCCCAGGAATGTATCATAAGAGGAGAAGCAGAGAAAAGCTACACTCCTGGCC
CAGTATGCTGATGTGACAGATGCAGAGGATGAGAAGGATGATAAGAATGATTCAGGTGCTACCACGATGAACGTTGCTCT
GATAAATCTGTATCCCAAAACAACAGTGTGGAAGATGTCTTTAATGCCAGAAAACGAGTGAGACTCGCTTTGGGATGAGT
CCCAAAGGAAGAAGGAACAGGACAAACTACAGAAGGAAAGGGACAAACTAGCTAAGTAGGAGTACAAGGAAAAGGAAGAG
GAAAGGGCACAAAGATGGGAGTGGAAGCAA

Alignment

ORF - retro_amel_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAPSEVAAAAPGEDD--GGGSG-FGSWLDGRLEALGVDRAVYGAYILGVLQEEEEEEKLDALQGILSAF
          MAAPSEV.AAA.GE.D..G.G.G....W.D.R.EALGVD.A..G...LGVLQEEEEEEKLD.LQGILSAF
Retrocopy MAAPSEVIAAALGEGDGGGSGFG>LDLWIDRRFEALGVD*AI-GHLHLGVLQEEEEEEKLDTLQGILSAF

Parental  LEEDSLLNVCKEIVERWSETIRRMALTAENSNYEVQAIATLIEKQAQIVVKPRMVSEEEKQRKAALLAQY
          LEEDSL.N.CKEIVERWSE......LT......E...IAT.I.KQ.QIVVKPR.VS.EEKQRKA.LLAQY
Retrocopy LEEDSL-NICKEIVERWSES--QNVLTKVKKEDEIEVIAT*I*KQGQIVVKPRNVS*EEKQRKATLLAQY

Parental  ADVTDEMLTEADEKDDSCATTINIG-SDKSLFRNTNVEDVLNARKLERDSL-RDESQRKKEQDKLQRERD
          ADVTD....E.D.K.DS.ATT.N...SDKS...N..VEDV.NARK..R..L.......K.EQDKLQ.ERD
Retrocopy ADVTDAE-DEKDDKNDSGATTMNVA<SDKSVSQNNSVEDVFNARKRVRLAL>DESQRKK-EQDKLQKERD

Parental  KLAKQERKEKEKKRTQRGERKR
          KLAK.E.KEKE..R.QR.E.K.
Retrocopy KLAK*EYKEKEEERAQRWEWKQ

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_1479 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1479 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018379	1 retrocopy	retro_amel_1479 ,
Canis familiaris	ENSCAFG00000014115	1 retrocopy	retro_cfam_456,
Monodelphis domestica	ENSMODG00000011411	1 retrocopy	retro_mdom_1378,
Mustela putorius furo	ENSMPUG00000009224	1 retrocopy	retro_mputfur_1511,
Oryctolagus cuniculus	ENSOCUG00000017526	1 retrocopy	retro_ocun_1500,
Ochotona princeps	ENSOPRG00000006793	2 retrocopies	retro_opri_263, retro_opri_699,
Rattus norvegicus	ENSRNOG00000002748	1 retrocopy	retro_rnor_2906,
Sus scrofa	ENSSSCG00000017352	2 retrocopies	retro_sscr_173, retro_sscr_944,