RetrogeneDB ID: retro_amel_1236

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193082.1:418924..419470(+)
• Located in intron of: ENSAMEG00000008620

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPS2
• Ensembl ID: ENSAMEG00000016576
• Aliases: None
• Description: None

Sequence

>retro_amel_1236
CCTCCTGCAGCGTCCCAAGCTTCCCGCCGCCTTGGCCGGGCGTTGCCCCGGGACATCAAGATGGAGCCTGAGCGCAAAGG
GCCGGAGGGGGAAGAGGGGGCCAAGCTGGTGGAGCAGAAGAGAAGGAAGAAAAAGGAGATAGAAGAGAGAATGTCACTAA
AGGAGCCCACAGAACAAATCCTGAAGTGGCAGGAGAAGCTTTGGGCCCTAGAGGAAGAGAAGCACCAGCTTTTCCTGCAG
CTCTAGAAAGTTTTACGGGAGGAAGAGAAGCGGACGCGAAAGGAGCAGAGTGACCTGAGCGCTCCGACAACAGCTGCGCC
TCCGCAGCGCCTGGACGTTCACACAGGAACTCACCTTCTCCGCGTGCAGACGAGCCCTTGGAGGACACAGTCACCCAGGC
ACCTCATGGCGGCTGACAGGGCCAAACAGAAGTGCGGGCCCCAAGCGCTTAGAACCTGGCACTACGTGGGCTCAGCAGCT
GCTTTCGCAGGGAGCCCAGGGCACGGTCCATTCCAAGGCAGCCCCCGCGGTGCCTATGGAACCGCC

Alignment

ORF - retro_amel_1236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.59 %
• Parental protein coverage: 56.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKLSNAMARALHRHIMMERERKRQEEEEVDKMMEQKMKEEQERRKKKEMEERMSLEETKEQILKLQEKLL
          P.......R.L.R.....R..K...E.......E.....EQ.RRKKKE.EERMSL.E..EQILK.QEKL.
Retrocopy PPAASQASRRLGR--ALPRDIKMEPERKGPEGEEGAKLVEQKRRKKKEIEERMSLKEPTEQILKWQEKLW

Parental  ALQEEKHQLFLQLKKVLHEEEKRRRKEQSDLTTLTSAAYPQSLTVHTGTHLLSMQGSP-GGHSRPGT-LM
          AL.EEKHQLFLQL.KVL.EEEKR.RKEQSDL...T.AA.PQ.L.VHTGTHLL..Q.SP.GGHS.PGT.LM
Retrocopy ALEEEKHQLFLQL*KVLREEEKRTRKEQSDLSAPTTAAPPQRLDVHTGTHLLRVQTSP>GGHSHPGT<LM

Parental  AADRAKQMFGPQVLTTRHYVGSAAAFAGTPEHGQFQGSPGGAYGTA
          AADRAKQ..GPQ.L.T.HYVGSAAAFAG.P.HG.FQGSP.GAYGTA
Retrocopy AADRAKQKCGPQALRTWHYVGSAAAFAGSPGHGPFQGSPRGAYGTA

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_1236 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1236 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016576	2 retrocopies	retro_amel_1236 , retro_amel_362,
Equus caballus	ENSECAG00000010635	2 retrocopies	retro_ecab_124, retro_ecab_480,
Homo sapiens	ENSG00000132522	2 retrocopies	retro_hsap_2738, retro_hsap_4222,
Gorilla gorilla	ENSGGOG00000001672	1 retrocopy	retro_ggor_1907,
Macropus eugenii	ENSMEUG00000010645	2 retrocopies	retro_meug_1327, retro_meug_182,
Myotis lucifugus	ENSMLUG00000026169	1 retrocopy	retro_mluc_1045,
Mus musculus	ENSMUSG00000023170	1 retrocopy	retro_mmus_1476,
Nomascus leucogenys	ENSNLEG00000009364	2 retrocopies	retro_nleu_2477, retro_nleu_600,
Pan troglodytes	ENSPTRG00000023046	1 retrocopy	retro_ptro_1852,
Pteropus vampyrus	ENSPVAG00000005052	1 retrocopy	retro_pvam_35,
Sus scrofa	ENSSSCG00000017940	1 retrocopy	retro_sscr_742,