RetrogeneDB ID: retro_amel_1453

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193416.1:305879..306612(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSAMEG00000001595
• Aliases: None
• Description: None

Sequence

>retro_amel_1453
AGTGTTAAATTTAACCCAATTGAGACATTTCTCTTGGGAAGTCATGCTTCTGACAGGAATATAGTGCTTTATGATATGAG
GCAAACTACTCCTCTGAAAAAGGTCATTTTAGAGATGAGAACAAATACAATTTGTTGGAACCCTATGGAAGCTTTCATTT
TTACTGCAGCAAATGAATATCACAACTTACATACTTTTGATATGCATGCACTGTACGCTCTAGTAATGGTACACGTGGAT
CACGTATCTGCAGTGCTTGAAGCGGATCATTCTCCCACTAGGAAAGAATTTGTGTCTGCTAGTTTTGATAAATTGATTTG
AATCTTTCCTGTGGACAAAAATAGAAGCAGGGAAGTCTATAACACAAAAAGAATGCAGCATGTTATCTGAGTAAAATGGA
CTTCTAACAGCAAATATATTATGAGTGGATCTGATGAAATGAATATTTGTCCATGGAAACCTAATGCTTCTGAAAAATTG
GGTGTGCTTACATCACGAGAAAAAGCAGGCAAAGATTATAACCAGAAATTGAAGGAGAAATTTCAACATCATCCTCATAT
AAAATGCATTGCTTGTCACCAATATCTATCAAAGTCTATCTACAGCCAGATCCAGGAACAGCACATCATGAAAGAAGCTT
GTCAACGAAAGGAAGTGAATCATCTCAAACAGAAAGCCTGGATCTGTGTAGATTGCGTCAGAAAAGAAGAAATACATAGT
GGCAGTTGTGAAA

Alignment

ORF - retro_amel_1453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 54.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVKFNPIETFLLGSCASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANEDYNLYTFDMRA
          SVKFNPIETFLLGS.ASDRNIVLYDMRQ.TPLKKVIL.MRTNTICWNPMEAFIFTAANE..NL.TFDM.A
Retrocopy SVKFNPIETFLLGSHASDRNIVLYDMRQTTPLKKVILEMRTNTICWNPMEAFIFTAANEYHNLHTFDMHA

Parental  LDTPVMVHMDHVSAVLDVDYSPTGKEFVSASFDKSTCIFPVDKSRSREVYHTKRMQHVICVKWTSDSKYI
          L...VMVH.DHVSAVL..D.SPT.KEFVSASFDK...IFPVDK.RSREVY.TKRMQHVI.VKWTS.SKYI
Retrocopy LYALVMVHVDHVSAVLEADHSPTRKEFVSASFDKLI*IFPVDKNRSREVYNTKRMQHVI*VKWTSNSKYI

Parental  MCGSDEMNIHLWKANASEKLGVLTSREKAGKDYNQKLKEKFQHHPHIKRIARHRHLPKSIYSQIQEQRIM
          M.GSDEMNI..WK.NASEKLGVLTSREKAGKDYNQKLKEKFQHHPHIK.IA.H..L.KSIYSQIQEQ.IM
Retrocopy MSGSDEMNICPWKPNASEKLGVLTSREKAGKDYNQKLKEKFQHHPHIKCIACHQYLSKSIYSQIQEQHIM

Parental  KEARRRKEVNRLKHSKPGSVSIV-SEKKKHIVAIVK
          KEA..RKEVN.LK......V..V...KK..IVA.VK
Retrocopy KEACQRKEVNHLKQKAWICVDCV>EKKK-YIVAVVK

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_1453 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1453 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001595	3 retrocopies	retro_amel_1453 , retro_amel_1723, retro_amel_399,
Canis familiaris	ENSCAFG00000000663	3 retrocopies	retro_cfam_1309, retro_cfam_1533, retro_cfam_305,
Callithrix jacchus	ENSCJAG00000016181	2 retrocopies	retro_cjac_3083, retro_cjac_612,
Felis catus	ENSFCAG00000027256	1 retrocopy	retro_fcat_1840,
Homo sapiens	ENSG00000164934	1 retrocopy	retro_hsap_1498,
Gorilla gorilla	ENSGGOG00000015124	1 retrocopy	retro_ggor_1150,
Myotis lucifugus	ENSMLUG00000007375	1 retrocopy	retro_mluc_2048,
Nomascus leucogenys	ENSNLEG00000003791	1 retrocopy	retro_nleu_1718,
Otolemur garnettii	ENSOGAG00000002277	1 retrocopy	retro_ogar_305,
Pongo abelii	ENSPPYG00000018809	2 retrocopies	retro_pabe_1249, retro_pabe_3211,
Pan troglodytes	ENSPTRG00000020493	1 retrocopy	retro_ptro_1017,
Sarcophilus harrisii	ENSSHAG00000006588	1 retrocopy	retro_shar_507,