RetrogeneDB ID: retro_amel_1928

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL208611.1:1..504(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHB2
• Ensembl ID: ENSAMEG00000013760
• Aliases: None
• Description: None

Sequence

>retro_amel_1928
CTGCAGATGCTGTCTCAACCCAACGCCATGGAACCTCCCAGCATGTACCAGTGCCTAGGGCTAGACTAGGAGGAATGAGG
ACTGCCATCAACTGTCAAGGAGGTGCTCAAGGGTGGCGTGGCCAAGTTCAACACCTCGCAGCCGATTACACAGCAGGCCC
AGATATCCTTGTTGATCTCGTGGGAGCTGACACAGAGGGCCAAGGAATTCAGGCTTATCCTGGATGATGTAGTCATCACA
GAGCTGAGTTTTAGCTGAGAGAGTACCCAGCTGCTACAGAAGCCAAACAAGTAGCTCATCAGAAAGTCCAGGGAGCCCAG
TTTTAGGTGGAAAAAGCAAAGCAGGAAGAGCAGCAGAAGACTGTGTAGGCTGAAGGTGAGGCTGAGGCCGCCACGATGCT
TGGAGAAGCCCTGACTGAGAATCCTGGCTACATCAAACTGGGCAAGATCCAGGCAGCCCAGAACATCTTCAAGACAACTG
CCACATCACAGAACTGTATCTAT

Alignment

ORF - retro_amel_1928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.68 %
• Parental protein coverage: 55.85 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRVLSRPNAMELPSMYQRLGLDYEERVLPSIVNEVLKSVVAKFNASQLITQRAQVSLLIRRELTERAKDF
          L..LS.PNAME.PSMYQ.LGLD.EE..LPS.V.EVLK..VAKFN.SQ.ITQ.AQ.SLLI..ELT.RAK.F
Retrocopy LQMLSQPNAMEPPSMYQCLGLD*EE*GLPSTVKEVLKGGVAKFNTSQPITQQAQISLLISWELTQRAKEF

Parental  SLILDDVAITELSFSREYTAAVE-AKQVAQQEAQRAQFLVEKAK-QEQRQKIVQAEGEAEAARMLGEALS
          .LILDDV.ITELSFS.E.T............E......L..K.K.QE..QK.V.AEGEAEAA.MLGEAL.
Retrocopy RLILDDVVITELSFS*ESTQLLQ>SQTSSSSESPGSPVLGGKSK>QEEQQKTV*AEGEAEAATMLGEALT

Parental  KNPGYIKLRKIRAAQNISKTIATSQNRIY
          .NPGYIKL.KI.AAQNI.KT.ATSQN.IY
Retrocopy ENPGYIKLGKIQAAQNIFKTTATSQNCIY

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_1928 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1928 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013760	1 retrocopy	retro_amel_1928 ,
Canis familiaris	ENSCAFG00000014439	1 retrocopy	retro_cfam_1885,
Callithrix jacchus	ENSCJAG00000007137	1 retrocopy	retro_cjac_781,
Homo sapiens	ENSG00000215021	1 retrocopy	retro_hsap_624,
Gorilla gorilla	ENSGGOG00000004281	1 retrocopy	retro_ggor_547,
Macaca mulatta	ENSMMUG00000010205	2 retrocopies	retro_mmul_2599, retro_mmul_2623,
Nomascus leucogenys	ENSNLEG00000005021	2 retrocopies	retro_nleu_121, retro_nleu_450,
Pongo abelii	ENSPPYG00000004214	3 retrocopies	retro_pabe_419, retro_pabe_557, retro_pabe_559,
Rattus norvegicus	ENSRNOG00000012999	1 retrocopy	retro_rnor_2373,