RetrogeneDB ID: retro_amel_1620

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193759.1:79623..80049(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEA1
• Ensembl ID: ENSAMEG00000012655
• Aliases: None
• Description: male-enhanced antigen 1 [Source:HGNC Symbol;Acc:6986]

Sequence

>retro_amel_1620
GCAGCAGTGTTTTTATGGGGAAGTGACCTGGGTCCGGAGCCTACCTTCCCCAACCAGTCTGAGGAACTGGGGCCACACCA
GAGCCCCGCATAAGGTATGGGGGTTAGAGCAGTGAGAAACCTGAGGAAGAACAGGAGGAAGGAGGACGTGGGATGAGGCC
CAGCTGGCTACTCCTACCAGCCCCTGAACCAAGATGCTGAACCAGAGGCGGCAGAGCTGGCACCTTGGGGGATGGAGACG
ATGTCGCTGCTGACACACAGCACTGGCTTCAGGTCCTGGGGCTTCACAGGCCAGACGTGCAGTTAAGAGTGAGGAGGAAG
ATGGAAAGGGAGCAGCAGCTCAGAGCAACCACAGCTCTCTCCCACGGACCCAGAACAAGCCGAGCTGGTGGGAAGGGCAA
AGGCTGAAGGTACAGAATTTCCAGCC

Alignment

ORF - retro_amel_1620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.78 %
• Parental protein coverage: 80.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AAVVLGGDTMGPERIFPNQTEELGPHQGPTEGTG-DWSSEEP--EEEQ-EETGAGPAGYSYQPLNQDPEQ
          AAV.L.G...GPE..FPNQ.EELGPHQ.P..G.G...SSE.P..E.E..E..G.GPAGYSYQPLNQD.E.
Retrocopy AAVFLWGSDLGPEPTFPNQSEELGPHQSPA*GMG<G*SSEKPEEEQEE>EDVG*GPAGYSYQPLNQDAEP

Parental  EEVELAP-VGDGEDVVADIQDRIQALGLHLPDPPL-ESEDEE-EGATGLSNHSSI-PMDPEHVELVKRTM
          E..ELAP..GDG.DV.AD.Q...Q.LGLH.PD..L..SE.E...GA...SNHSS..P.DPE..ELV.R..
Retrocopy EAAELAP<LGDGDDVAADTQHWLQVLGLHRPDVQL<KSEEEDGKGAAAQSNHSSL<PTDPEQAELVGRAK

Parental  A-GVSLPA
          A.G...PA
Retrocopy AEGTEFPA

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_1620 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1620 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 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012655	1 retrocopy	retro_amel_1620 ,
Bos taurus	ENSBTAG00000005536	1 retrocopy	retro_btau_240,
Canis familiaris	ENSCAFG00000001756	1 retrocopy	retro_cfam_1643,
Callithrix jacchus	ENSCJAG00000004894	2 retrocopies	retro_cjac_2054, retro_cjac_824,
Cavia porcellus	ENSCPOG00000022111	1 retrocopy	retro_cpor_1530,
Echinops telfairi	ENSETEG00000002439	1 retrocopy	retro_etel_236,
Felis catus	ENSFCAG00000031337	1 retrocopy	retro_fcat_1772,
Loxodonta africana	ENSLAFG00000013881	1 retrocopy	retro_lafr_60,
Myotis lucifugus	ENSMLUG00000012138	2 retrocopies	retro_mluc_1819, retro_mluc_851,
Monodelphis domestica	ENSMODG00000019002	1 retrocopy	retro_mdom_878,
Oryctolagus cuniculus	ENSOCUG00000001565	2 retrocopies	retro_ocun_1312, retro_ocun_1446,
Pelodiscus sinensis	ENSPSIG00000002330	1 retrocopy	retro_psin_56,
Pteropus vampyrus	ENSPVAG00000008711	1 retrocopy	retro_pvam_266,
Rattus norvegicus	ENSRNOG00000017144	2 retrocopies	retro_rnor_716, retro_rnor_961,
Tupaia belangeri	ENSTBEG00000012294	2 retrocopies	retro_tbel_1462, retro_tbel_3528,
Tursiops truncatus	ENSTTRG00000006996	1 retrocopy	retro_ttru_357,