RetrogeneDB ID: retro_amel_1531

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193562.1:229186..229841(+)
• Located in intron of: ENSAMEG00000018240

Retrocopy information

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

Parental gene information

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

Sequence

>retro_amel_1531
GGGGCTAATGAGGACTCCCTCATTGACATTATCTCCTCAAGGACCAACCAAGAGCTTCAGGAAATAACAAAGTCTACAAG
AAAATGTACAAGACTGATCTGAGAAGGACATCATTTCTGACATATCTGGTGACTTCCGCAAGCTGATGGTTGCCCTTGCA
AAGGGTAGAAGAGCAGAGGACGGCTCTGTCATTGATTATGAACTGACTGACCAAGATGCCTGGGATCTCTATGATGGTGG
AGTGAAGAGGAAAGGAACTGATGTGCCCAAGTGGATCAGCATCATGACCAAGCAGAGTGTGTGTCACCTCCAGAAAGTAT
TTGAAAGGTACAAGAGCTACAGCCCTCGTGACCCACTGGAGAGCATCAAGGAGGTCAAAGGAGACCTGGAAAACGCTTTC
CTGAACTGGGTCCAGAGCATTCAGAACAAGCCCCTGTATTTTGCTGACTGACTGTACAACTCCATGAAAGGCAAGGGGAC
TTGCAATAATAAATTAGAATCATAATCTATCATGACCTCTCGCAGTGAAGCAGACATGCGGAAAATTAGGTCTGAATTCA
AGAGAAAGTACAGCAAGTCCCTGTACTACTGCATCCAGCAAGACACCAAGGGCGACTGCCAGAAAGCACTGCTATACCTG
TGTGGTGGGGATGAC

Alignment

ORF - retro_amel_1531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.23 %
• Parental protein coverage: 63.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GTDEDSLIEIICSRTNQELQEI-NRVYKEMYKTDL-EKDIVSDISGDFRKLMVALAKGRRAEDGSVIDYE
          G..EDSLI.II.SRTNQELQEI.N.VYK.MYKTDL.EKDI.SDISGDFRKLMVALAKGRRAEDGSVIDYE
Retrocopy GANEDSLIDIISSRTNQELQEI<NKVYKKMYKTDL<EKDIISDISGDFRKLMVALAKGRRAEDGSVIDYE

Parental  LIDQDARDLYDAGVKRKGTDVPKWISIMTERSVCHLQKVFERYKSYSPYDMLESIKKEVKGDLENAFLNL
          L.DQDA.DLYD.GVKRKGTDVPKWISIMT..SVCHLQKVFERYKSYSP.D.LESI.KEVKGDLENAFLN.
Retrocopy LTDQDAWDLYDGGVKRKGTDVPKWISIMTKQSVCHLQKVFERYKSYSPRDPLESI-KEVKGDLENAFLNW

Parental  VQCIQNKPLYFADRLYDSMKGKGTRDKVLI--RIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDY
          VQ.IQNKPLYFAD.LY.SMKGKGT....L....IM.SRSE.DM.KIRSEFKRKY.KSLYY.IQQDTKGD.
Retrocopy VQSIQNKPLYFAD*LYNSMKGKGTCNNKLES*SIMTSRSEADMRKIRSEFKRKYSKSLYYCIQQDTKGDC

Parental  QKALLYLCGGDD
          QKALLYLCGGDD
Retrocopy QKALLYLCGGDD

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_1531 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1531 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,