RetrogeneDB ID: retro_amel_1003

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192812.1:1059520..1060049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000005805
• Aliases: None
• Description: None

Sequence

>retro_amel_1003
GCTCATGGTCCCAAGAGCCTCTGAAGCACATAGCAGCTCCAAGGCATTGGATGCTGGATAAACTGACCGGTGTGTTGCCC
TCGTCCGGTCCCCAGAAGCAGAGAGAATGTCTCCTTCTCATCATTTCCCAAAGGAACAGACTGTAGTATGCCCTAACAGG
GGGTGAAGTGAAAAAGATCTGTTTTCAGTGTTTTATTAAGGTCGATGGCAAGGTCTGAACTGGTATAACCTACCTGCTGG
TTTGATGGATGTCATCAGCATTGACAAGACTGAGAAGAATGTCCATCTGATCCATGACACCCAGGGTTGCTTTGCTGTTC
GTCGGATTACACCTGAGGAGGCCCAGTATAAGTTGTGCAAAGTGAGAAAGATCTTTGTGGGGACAAATGAAATCCCTCAT
CTGGTGAGCCATCGTGCTCACACCATCTGCTATCCTGATCCCCTCGTCAAAGTGAATGACACCATTCAGATTGATTTGGA
GACTGGAAAGATTGCTGATTTCATCAAGTTTGACACCGGTAATCTGTGT

Alignment

ORF - retro_amel_1003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.37 %
• Parental protein coverage: 66.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARGPK-KHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRFI
          A.GPK...LK..AAP.HWMLDKLTGV....PS.GP.K.RECL.LII..RNRL.YALTG.EVKKIC.Q.FI
Retrocopy AHGPK<EPLKHIAAPRHWMLDKLTGVL---PSSGPQKQRECLLLIISQRNRL*YALTGGEVKKICFQCFI

Parental  KIDGKVRTDITY-PAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
          K.DGKV.T.ITY.PAG.MDVISIDKT..N..LI.DT.G.FAV.RITPEEA.YKLCKVRKIFVGT..IPHL
Retrocopy KVDGKV*TGITY<PAGLMDVISIDKTEKNVHLIHDTQGCFAVRRITPEEAQYKLCKVRKIFVGTNEIPHL

Parental  VTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLC
          V.H.A.TI.YPDPL.KVNDTIQIDLETGKI.DFIKFDTGNLC
Retrocopy VSHRAHTICYPDPLVKVNDTIQIDLETGKIADFIKFDTGNLC

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_1003 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1003 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 18 parental genes, and 125 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Ailuropoda melanoleuca	ENSAMEG00000005805	14 retrocopies	retro_amel_1003 , retro_amel_1128, retro_amel_1296, retro_amel_1381, retro_amel_1695, retro_amel_1869, retro_amel_195, retro_amel_259, retro_amel_327, retro_amel_576, retro_amel_767, retro_amel_869, retro_amel_968, retro_amel_971,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Gorilla gorilla	ENSGGOG00000023079	18 retrocopies	retro_ggor_1278, retro_ggor_1319, retro_ggor_1354, retro_ggor_1367, retro_ggor_1478, retro_ggor_1479, retro_ggor_1517, retro_ggor_1520, retro_ggor_1689, retro_ggor_223, retro_ggor_2676, retro_ggor_2719, retro_ggor_572, retro_ggor_711, retro_ggor_844, retro_ggor_894, retro_ggor_895, retro_ggor_939,
Loxodonta africana	ENSLAFG00000002654	4 retrocopies	retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii	ENSMEUG00000007969	16 retrocopies	retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Procavia capensis	ENSPCAG00000000761	3 retrocopies	retro_pcap_334, retro_pcap_35, retro_pcap_360,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Pteropus vampyrus	ENSPVAG00000012882	21 retrocopies	retro_pvam_1021, retro_pvam_1082, retro_pvam_1158, retro_pvam_1264, retro_pvam_1298, retro_pvam_1312, retro_pvam_1327, retro_pvam_1364, retro_pvam_1419, retro_pvam_177, retro_pvam_191, retro_pvam_214, retro_pvam_219, retro_pvam_335, retro_pvam_473, retro_pvam_628, retro_pvam_714, retro_pvam_809, retro_pvam_835, retro_pvam_921, retro_pvam_930,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Ictidomys tridecemlineatus	ENSSTOG00000028692	8 retrocopies	retro_itri_1179, retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368, retro_itri_495, retro_itri_738, retro_itri_985,
Tursiops truncatus	ENSTTRG00000006164	13 retrocopies	retro_ttru_104, retro_ttru_1104, retro_ttru_1129, retro_ttru_1748, retro_ttru_260, retro_ttru_465, retro_ttru_470, retro_ttru_512, retro_ttru_565, retro_ttru_618, retro_ttru_631, retro_ttru_728, retro_ttru_734,