RetrogeneDB ID: retro_amel_376

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192411.1:670614..670963(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1G1
• Ensembl ID: ENSAMEG00000012509
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G1 [Source:HGNC Symbol;Acc:864]

Sequence

>retro_amel_376
ATGGCCAATCAGTCACAGGCTTTACAGCAGCTTCTACAGGCTGAGAAGTGGGTGCCCAGAAAGTGTCCAAGGTCCACATG
CAAAAAGAAATGGAAGCTGAAGCAAGTCAAAGCACCTCAAGCTGGAACAGAATGGTACAGCCTGCAAAGAGAGAAAAGTG
TCCAAGGCTGAGGAAATGGCAGCTCTGGGATCCCATGGCAGGGGCAGTACTGAAGTGGAGAAGAAGATTCAATAGATGAT
GACCACCCTCCAGACCTAATACCAGCAAAACAGGGATTAAGTCCTAGATAACCTCTTGGCCTTTAAGATATCAACCAGAA
CAGAAATCCATGAAAACTACCGCCTAAAT

Alignment

ORF - retro_amel_376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.32 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASQSQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEF-KAKEAAALGSHGSC
          MA.QSQ..QQLLQAEK....K.......K...LKQ.K...QA..E.Y.LQREK...KA.E.AALGSHG..
Retrocopy MANQSQALQQLLQAEKWVPRKCPRSTCKKKWKLKQVKAP-QAGTEWYSLQREKSV>KAEEMAALGSHGRG

Parental  STEVEKETQEKMTVLQKYFQQNRDEVLDNLLAFVCDIRPEIHENYRIS
          STEVEK..Q..MT.LQ...QQNRD.VLDNLLAF....R.EIHENYR..
Retrocopy STEVEKKIQ*MMTTLQT*YQQNRD*VLDNLLAFKISTRTEIHENYRLN

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_376 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_376 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 13 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012509	3 retrocopies	retro_amel_1053, retro_amel_376 , retro_amel_999,
Callithrix jacchus	ENSCJAG00000020461	3 retrocopies	retro_cjac_1788, retro_cjac_2513, retro_cjac_76,
Dasypus novemcinctus	ENSDNOG00000008083	15 retrocopies	retro_dnov_1173, retro_dnov_1447, retro_dnov_1475, retro_dnov_1504, retro_dnov_1588, retro_dnov_1645, retro_dnov_193, retro_dnov_1998, retro_dnov_2179, retro_dnov_218, retro_dnov_2416, retro_dnov_245, retro_dnov_336, retro_dnov_479, retro_dnov_790,
Dipodomys ordii	ENSDORG00000014850	5 retrocopies	retro_dord_434, retro_dord_466, retro_dord_614, retro_dord_640, retro_dord_749,
Echinops telfairi	ENSETEG00000008080	3 retrocopies	retro_etel_350, retro_etel_594, retro_etel_996,
Felis catus	ENSFCAG00000000160	2 retrocopies	retro_fcat_1614, retro_fcat_402,
Loxodonta africana	ENSLAFG00000013437	2 retrocopies	retro_lafr_1002, retro_lafr_39,
Myotis lucifugus	ENSMLUG00000008657	2 retrocopies	retro_mluc_373, retro_mluc_839,
Macaca mulatta	ENSMMUG00000004899	4 retrocopies	retro_mmul_1783, retro_mmul_2018, retro_mmul_2046, retro_mmul_331,
Monodelphis domestica	ENSMODG00000019574	1 retrocopy	retro_mdom_1675,
Mustela putorius furo	ENSMPUG00000001653	3 retrocopies	retro_mputfur_1338, retro_mputfur_922, retro_mputfur_994,
Mus musculus	ENSMUSG00000039105	5 retrocopies	retro_mmus_2028, retro_mmus_2784, retro_mmus_2787, retro_mmus_3316, retro_mmus_819,
Oryctolagus cuniculus	ENSOCUG00000026252	3 retrocopies	retro_ocun_1411, retro_ocun_368, retro_ocun_639,