RetrogeneDB ID: retro_amel_1794

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194355.1:21824..22228(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000007221
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSAMEG00000009765
• Aliases: None
• Description: H3 histone, family 3B (H3.3B) [Source:HGNC Symbol;Acc:4765]

Sequence

>retro_amel_1794
GCTGGCGCAAAGCAGACTGCCCACAAATCCACCAGTGGTAAAGCAACAAGGAAGCCACTGGATACAAAAGCCACAGGCAA
GAGTGCGCCCTCTACTGAGGGGTAAAGAAACCTCATCATTACAGGCCTGGTGCTGCGGCACTCGGTGAAATTAGACATTA
TCAGAAGTCCACTGAGCACCTGAGCCACAAACTTCCCTTCCAGCGGCTGGTGCGAGAAACTGCTCAGGTCTTCGGAACAG
GTCTGTGCTTCCAGAGGCCAGCTATTGGTGCTTTGCTGGAGGCACGTGAGGCCTATCTGGCGGACCTTTCTGAAGACACC
AACCTGTGTGCTGTCCATGACAAACACGTCACAACTATGCCAAAAGACATCCAGCTAGCATGCCGCATACGTGGAGAATG
TGCT

Alignment

ORF - retro_amel_1794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.79 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARTKQTARKSTGGKAPRKQLATKAARKSAPSTG-GVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          A..KQTA.KST.GKA.RK.L.TKA..KSAPST..GVKKPH.YRPG..AL.EIR.YQKSTE.L..KLPFQR
Retrocopy AGAKQTAHKSTSGKATRKPLDTKATGKSAPSTE<GVKKPHHYRPGAAALGEIRHYQKSTEHLSHKLPFQR

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVRE.AQ.F.T.L.FQ..AIGAL.EA.EAYL..L.EDTNLCA.H.K.VT.MPKDIQLA.RIRGE.A
Retrocopy LVRETAQVFGTGLCFQRPAIGALLEAREAYLADLSEDTNLCAVHDKHVTTMPKDIQLACRIRGECA

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_1794 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1794 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 84 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009765	3 retrocopies	retro_amel_1636, retro_amel_1794 , retro_amel_192,
Ailuropoda melanoleuca	ENSAMEG00000014588	7 retrocopies	retro_amel_1023, retro_amel_1026, retro_amel_144, retro_amel_570, retro_amel_687, retro_amel_711, retro_amel_903,
Choloepus hoffmanni	ENSCHOG00000009661	10 retrocopies	retro_chof_1580, retro_chof_1635, retro_chof_1911, retro_chof_2281, retro_chof_2294, retro_chof_2343, retro_chof_2546, retro_chof_454, retro_chof_517, retro_chof_530,
Cavia porcellus	ENSCPOG00000004707	7 retrocopies	retro_cpor_1059, retro_cpor_1390, retro_cpor_1524, retro_cpor_432, retro_cpor_695, retro_cpor_842, retro_cpor_853,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Mus musculus	ENSMUSG00000060743	19 retrocopies	retro_mmus_1053, retro_mmus_1116, retro_mmus_1139, retro_mmus_1151, retro_mmus_1254, retro_mmus_2285, retro_mmus_2614, retro_mmus_2934, retro_mmus_3009, retro_mmus_3213, retro_mmus_3425, retro_mmus_395, retro_mmus_498, retro_mmus_808, retro_mmus_884, retro_mmus_885, retro_mmus_886, retro_mmus_959, retro_mmus_960,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449, retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,