RetrogeneDB ID: retro_amel_1919

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL196493.1:5585..6600(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000001235
• Aliases: None
• Description: None

Sequence

>retro_amel_1919
AGGGTGATACCAGCTGACCTCAAGTGAATGGCCAACAACTGGCAGCCAGAAAATGAAAAGGAAGCTTCTGGTGGAGACAG
CCCCAAGGGGGATTCAAAGCCACCTTATTCCTACGCAGAAATCATAGGACAGAAAACTACGATGGCTGCTGAGAACAACG
TACCCTAAATGGTATTTATACTCACATCACTAAAAATGATCCATACTACAAGACAGCGGACAAGAGCTGGCCGAATCCAA
TTCGCCACAATCTCTCTCTGAATCCTTATTTCATCATAGTACCACGTTCCCAGGAAGAACCAGGCAAAAGGGCTCATTCC
GAGGACAGATCCTGCCTCTGAAAGCAAATTCATAGAGCAGGCTTTTAGGAAAAGACAGTCCATGACCATGCATTGCTTTA
GAAACCCTCCGGGGTACTTCTTCTCCAGAAGTGGCCCAGCCTCTCCCAATCACGCTGGAGTGCTGTCTGCACTCGCCAGT
GGTGCCCAGACCCCCAAGAGCCTGTCAAGGGAAGTTTTACCAGCCCCCCTGGAGCCTGAGCCCAGTGCCTCACAGCCCAA
ACTGGCCATCATCCAGGAGGCATGGTTTGCCCAGGGTGCACCAGGCTCCCCTCTGTCTTGTCAGCCCATTTTAATGGCCG
GGCAGTGGCAGCTGCCACCGACGATCGATCAATCCCATCACCTACACGGTCGCTGCTCCCGTGACCACCTCGACCTCCCA
GCAGCCTGTAGTGCAGACGGTGCACGTCGCCCACCAGATCCCCGCAGTGTCTGTCACCAGCAGGACAGGCCTGGCCCTGG
GAAGCATGAACACTGTCATCGTCCAGGCTCTGGTCACTCAGGCGGCTGTGCCGGCCCCTACTAAGGCAGAGCCGCCAGAC
AATGGAGATCACAAAGAAGTAAAAGTGAACGTGGAACCTATTCCTGCCATTACCCATGCCACAGCGGGTGCTGCCGGCTG
GATCATTCAGGAGCCCCAGACCACCCCTGTCCACACAGTCACCACAGCACAGCAG

Alignment

ORF - retro_amel_1919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.55 %
• Parental protein coverage: 62.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RVIPADLNIMADNSQPENEKEASGGDSPKDDSKPPYSYAQLIVQAITMAPD-KQLTLNGIYTHITKNYPY
          RVIPADL..MA.N.QPENEKEASGGDSPK.DSKPPYSYA..I.Q..TMA....Q.TLNGIYTHITKN.PY
Retrocopy RVIPADLK*MANNWQPENEKEASGGDSPKGDSKPPYSYAEIIGQKTTMAAE<EQRTLNGIYTHITKNDPY

Parental  YRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGK-GSFWRIDPASESKLIEQAFRKRRPRGVPCFRTPLG
          Y.TADK.W.N.IRHNLSLN.YFI.VPRSQEEPGK.G...R.DPASESK.IEQAFRKR......CFR.P.G
Retrocopy YKTADKSWPNPIRHNLSLNPYFIIVPRSQEEPGK>GLIPRTDPASESKFIEQAFRKRQSMTMHCFRNPPG

Parental  PLSSRSAPASPNHAGVLSAHSSGAQTPESLSREGSPAPLEPEPSASQPKLAVIQEARFAQSAPGSPLSSQ
          ...SRS.PASPNHAGVLSA..SGAQTP.SLSRE..PAPLEPEPSASQPKLA.IQEA.FAQ.APGSPLS.Q
Retrocopy YFFSRSGPASPNHAGVLSALASGAQTPKSLSREVLPAPLEPEPSASQPKLAIIQEAWFAQGAPGSPLSCQ

Parental  PVLIAVQRQLPPTIKPVTYT-VAAPVTTSTSQQ-PVVQTVHVVHQIPAVSVTSVAGLAPASTYTVAGQAV
          P.L.A.Q.QLPPTI.........A...T....Q.PVVQTVHV.HQIPAVSVTS..GLA..S..TV..QA.
Retrocopy PILMAGQWQLPPTIDQSHHL>TVAAPVTTSTSQQPVVQTVHVAHQIPAVSVTSRTGLALGSMNTVIVQAL

Parental  VTQAAVLAPPQAEPQENGDHKEVKVKVEPIPAMSHAALGAASRVIQTPQTTPVQTVTILQQ
          VTQAAV.AP..AEP..NGDHKEVKV.VEPIPA..HA..GAA...IQ.PQTTPV.TVT..QQ
Retrocopy VTQAAVPAPTKAEPPDNGDHKEVKVNVEPIPAITHATAGAAGWIIQEPQTTPVHTVTTAQQ

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_1919 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1919 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001235	1 retrocopy	retro_amel_1919 ,
Rattus norvegicus	ENSRNOG00000036663	1 retrocopy	retro_rnor_1560,