RetrogeneDB ID: retro_amel_355

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192399.1:1008434..1009195(+)
• Located in intron of: ENSAMEG00000007021

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF10
• Ensembl ID: ENSAMEG00000009869
• Aliases: None
• Description: serine/arginine-rich splicing factor 10 [Source:HGNC Symbol;Acc:16713]

Sequence

>retro_amel_355
AATACATCTCTCTTCATAAGGAACGTGGCCTATGACACCAGGTCTGAAGATTTACGACGAGAATTTGGTCGTTATGGTCC
TATAGTTGATGTGTATGTTCCACTTAATTTCTACATGCGCCGTCCAAGAGGATTTGCTTATGTTCAATTTGAGGATGTCC
ATGATGCCGAAGACGCTTTACATAATTTGGACAGAAAATGCATTTGTGGACGCCAAATTGAAATGCAGTTTGCACAGGGG
GATCGGAAAACTCCAAATCAGATGAAAGCCAAGGAAGGGAGGAATGTGTACAGTTCTTCACACTATGATGATTATGACAG
ATACAGACGTTCTAGAAGCCAGATTATGAAAGAGGAAGATCAAGAAGCCGGTCCTTTGATTACAACTAGAGGAGATCTTA
TAGTCCTAGAAGCAATAGACCGGTTGGAAGACCACGGCATAGCAGAAGCCATTCCATCAATGATAGATTCAAACACTGAA
ATCGATCTTTTTCAAGATCTAAATCCAATTCAAGATCACGGTCCAAGTCCCAGCCCAAGAAAGAAATGAAGGCTAAATCA
GGTTCTAGGTCTGCATCTCACACCAAAACTAGAGGCACCTCTAAAACAGATTCCAAAACACATTATAAGTCAAAAAAAAG
ATATGAAAAGGAATCAAGGAAAAAAGAACCACCTAGATCCAAATCTCAGTCAAGATCACAATCTAGGTCTAGGTCAAAAT
CTAGATCAAGGTCTTGGACTAGTCCTAAGTCCAGTGGCCAC

Alignment

ORF - retro_amel_355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.21 %
• Parental protein coverage: 96.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NTSLFVRNVADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQYTFEDVRDAEDALHNLDRKWI
          NTSLF.RNVA.DTRSEDLRREFGRYGPIVDVYVPL.FY.RRPRGFAYVQ..FEDV.DAEDALHNLDRK.I
Retrocopy NTSLFIRNVAYDTRSEDLRREFGRYGPIVDVYVPLNFYMRRPRGFAYVQ--FEDVHDAEDALHNLDRKCI

Parental  CGRQIEIQFAQGDRKTPNQMKAKEGRNVYSSSRYDDYDRYRRSRSR-SYERRRSRSRSFDYNYRRSYSPR
          CGRQIE.QFAQGDRKTPNQMKAKEGRNVYSSS.YDDYDRYRRSRS...YER.RSRSRSFDYN.RRSYSPR
Retrocopy CGRQIEMQFAQGDRKTPNQMKAKEGRNVYSSSHYDDYDRYRRSRSQ<DYERGRSRSRSFDYN*RRSYSPR

Parental  NSRPAGRPRRSRSHSDNDRFKHRNRSFSRSKSNSRSRSKSQPKKEMKAKSRSRSASHTKTRGAS--DSKT
          ..RP.GRPR.SRSHS.NDRFKH.NRSFSRSKSNSRSRSKSQPKKEMKAKS.SRSASHTKTRG.S..DSKT
Retrocopy SNRPVGRPRHSRSHSINDRFKH*NRSFSRSKSNSRSRSKSQPKKEMKAKSGSRSASHTKTRGTSKTDSKT

Parental  HCKSGSRYEKESRKKEPPRSKSQSRSQSRSRSKSRSRSWTSPKSSGH
          H.K............EPPRSKSQSRSQSRSRSKSRSRSWTSPKSSGH
Retrocopy HYKXXXXXXXXXXXXEPPRSKSQSRSQSRSRSKSRSRSWTSPKSSGH

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_355 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_355 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 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009869	2 retrocopies	retro_amel_1810, retro_amel_355 ,
Bos taurus	ENSBTAG00000008072	1 retrocopy	retro_btau_759,
Choloepus hoffmanni	ENSCHOG00000004836	1 retrocopy	retro_chof_7,
Callithrix jacchus	ENSCJAG00000020883	9 retrocopies	retro_cjac_1126, retro_cjac_1170, retro_cjac_2176, retro_cjac_2595, retro_cjac_2638, retro_cjac_3852, retro_cjac_628, retro_cjac_705, retro_cjac_864,
Cavia porcellus	ENSCPOG00000024533	1 retrocopy	retro_cpor_1098,
Dasypus novemcinctus	ENSDNOG00000008699	3 retrocopies	retro_dnov_1327, retro_dnov_1809, retro_dnov_2244,
Erinaceus europaeus	ENSEEUG00000014286	1 retrocopy	retro_eeur_522,
Homo sapiens	ENSG00000188529	5 retrocopies	retro_hsap_1343, retro_hsap_1940, retro_hsap_2445, retro_hsap_3054, retro_hsap_4295,
Gorilla gorilla	ENSGGOG00000000392	4 retrocopies	retro_ggor_1044, retro_ggor_1411, retro_ggor_1522, retro_ggor_2870,
Myotis lucifugus	ENSMLUG00000028520	1 retrocopy	retro_mluc_89,
Mustela putorius furo	ENSMPUG00000015845	1 retrocopy	retro_mputfur_353,
Nomascus leucogenys	ENSNLEG00000013180	3 retrocopies	retro_nleu_1647, retro_nleu_1825, retro_nleu_202,
Oryctolagus cuniculus	ENSOCUG00000029326	1 retrocopy	retro_ocun_717,
Otolemur garnettii	ENSOGAG00000015374	2 retrocopies	retro_ogar_2650, retro_ogar_2987,
Pongo abelii	ENSPPYG00000001726	4 retrocopies	retro_pabe_1115, retro_pabe_1601, retro_pabe_1796, retro_pabe_2529,
Rattus norvegicus	ENSRNOG00000007992	3 retrocopies	retro_rnor_1657, retro_rnor_2800, retro_rnor_2829,
Ictidomys tridecemlineatus	ENSSTOG00000000956	1 retrocopy	retro_itri_1333,
Tursiops truncatus	ENSTTRG00000016150	2 retrocopies	retro_ttru_1098, retro_ttru_695,