RetrogeneDB ID: retro_amel_1836

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194691.1:57643..58596(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000001551
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANXA2
• Ensembl ID: ENSAMEG00000008055
• Aliases: None
• Description: annexin A2 [Source:HGNC Symbol;Acc:537]

Sequence

>retro_amel_1836
CCAAGTGCACACGGGTGCGTCGAAGCATATACCAATGTGGAATGCTGAGTGTGATTCTCTGAACATTGCAACGCCATCAA
GAGCAAAGGTGTGGATGAGGTCATCATTGTCAACACCTGACCCACCACAGAAATATAGAGAGACAGGATATTGCCTTCAC
CTACCAGAGAAAGACCAAAAGGGACCTTGCATCACCACTGAAGTCAGCCTTGTCCAACCACCTGGAGACCATAGTTTGGG
CTTACTGAAAACATCTGCTCAGTACAATGCTTCTCAACTAAAAGCCTCCATGAGGCAGGAGACTGATGAGGACTCCCTCC
CTGAGATCATCTGCTCAAAGACCGACCAGGAGCTTCAGGAAATTAACAGAGTCTGCAAGGCAATGTACAAGACTGATCTG
GAGAAGGACATCATGTCTGACATATCTGATGACTTCTGCCAGCTGATGCTTGTCCTCGCAAAGGGTAAAAGAGCAGAAGA
TAGCTCTGTCATTGATTATGAACAGATTGACCAAGATACCCAGGATCTCTATGATGCTGGGGTGACGAGGAAAAGAACTG
ATGTGCCCAAGCCGATTGGCATCATGACTGAGCAGACTGTGTGTCACCTCCAAAAAGTATTTGGCAGGTATAAGAGCTAC
AGCCCTTATGACATGCTGAAGAGCATCAAGAAGGAGGTCAAAGGAGACTTGGAAGATGCTTTCCTGAGCCAGTCCAGTGC
ATTCAGAAAGAGCCCCTCTATTTTGCTGACCGACTGTACAACTCCATGAAAGGCAAAGAGACTTGCTGTAAAGTCCTGAT
TAGAATCATGGTCTCTTGCAGTGAAGTGAACATGTTAAAAGTTAGGTCTGAATTCAAGAGAGAGTATGACAAGTCCCTGA
ACTACCATATCCAGCAAGTCTACCAAGGGCGACTACCAGAAAGCACTGCTTATACCTGTCTGGTGGGGATGAC

Alignment

ORF - retro_amel_1836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.46 %
• Parental protein coverage: 93. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  PSAYGSVKAYTN-FDAERDALNIET-AIKTKGVDEVTIVNI-LTNRSNEQRQDIAFAYQRRTKKELASAL
          PSA.G.V.AYTN...AE.D.LNI.T.AIK.KGVDEV.IVN..LT...N..RQDIAF.YQR.TK..LAS.L
Retrocopy PSAHGCVEAYTN>WNAECDSLNIAT<AIKSKGVDEVIIVNT<LTHHRNIERQDIAFTYQRKTKRDLASPL

Parental  KSALSGHLETVI-LGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLE
          KSALS.HLET...LGLLKT.AQY.AS.LKASM....TDEDSL.EIICS.T.QELQEINRV.K.MYKTDLE
Retrocopy KSALSNHLETIV<LGLLKTSAQYNASQLKASMRQ-ETDEDSLPEIICSKTDQELQEINRVCKAMYKTDLE

Parental  KDIVSDISGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVCHLQ
          KDI.SDIS.DF..LM..LAKG.RAED.SVIDYE.IDQD..DLYDAGV.RK.TDVPK.I.IMTE..VCHLQ
Retrocopy KDIMSDISDDFCQLMLVLAKGKRAEDSSVIDYEQIDQDTQDLYDAGVTRKRTDVPKPIGIMTEQTVCHLQ

Parental  KVFERYKSYSPYDMLESIKKEVKGDLENAFLNL-VQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSR
          KVF.RYKSYSPYDML.SIKKEVKGDLE.AFL...VQCIQ..PLYFADRLY.SMKGK.T..KVLIRIMVS.
Retrocopy KVFGRYKSYSPYDMLKSIKKEVKGDLEDAFLSQ<VQCIQKEPLYFADRLYNSMKGKETCCKVLIRIMVSC

Parental  SEVDMLKIRSEFKRKYGKSLYYYIQQ-DTKGDYQKAL-LYLCGGDD
          SEV.MLK.RSEFKR.Y.KSL.Y.IQQ..TKGDYQKAL.LYL.GGDD
Retrocopy SEVNMLKVRSEFKREYDKSLNYHIQQ>STKGDYQKAL>LYLSGGDD

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_1836 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1836 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008055	2 retrocopies	retro_amel_1531, retro_amel_1836 ,
Bos taurus	ENSBTAG00000009615	2 retrocopies	retro_btau_634, retro_btau_985,
Canis familiaris	ENSCAFG00000016686	3 retrocopies	retro_cfam_1631, retro_cfam_367, retro_cfam_707,
Equus caballus	ENSECAG00000012670	1 retrocopy	retro_ecab_759,
Felis catus	ENSFCAG00000007862	2 retrocopies	retro_fcat_594, retro_fcat_709,
Macropus eugenii	ENSMEUG00000008980	3 retrocopies	retro_meug_1000, retro_meug_312, retro_meug_389,
Monodelphis domestica	ENSMODG00000011604	1 retrocopy	retro_mdom_1471,
Mustela putorius furo	ENSMPUG00000000762	2 retrocopies	retro_mputfur_73, retro_mputfur_79,
Pan troglodytes	ENSPTRG00000007132	2 retrocopies	retro_ptro_2106, retro_ptro_81,
Tursiops truncatus	ENSTTRG00000007705	1 retrocopy	retro_ttru_1725,