RetrogeneDB ID: retro_tbel_3447

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_141035:34512..34980(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPA1
• Ensembl ID: ENSTBEG00000001669
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide A' [Source:HGNC Symbol;Acc:11152]

Sequence

>retro_tbel_3447
TGTGTGATGGAACTGATTCTCATTAACAGTAGTCTTGTGGAACTGGGATCTTAGACCCTTTGACATCTCTCAAATCACTG
GCTTATCTAATTATTCTAAGAATTGCAGGAATAAACAAGAAACATTGAAGGTTACATGTTACTGTAAGGTGTCACGAGTC
AGAGTACTGGATATCTAGAAGGCCAAACTCAGCTTTTAGGAAGCAGAGAAAATGTTCAAGGGCAAAGAGGTTGCAAAGAA
TTTTGTTAGGAGAAACAACATGTTTAATCCAGGTATGGAGTTATCAATTGACAAAAAGAAAGGAAGGCCACCTCTAGGGG
AGGCAGAAGCAATCGAGAATGCGATAGCAAATGCATCCACTCTGGCTGCTGTGGAGAGGCTGCTGCAGAATGGTCAGATA
ACCTGGCAGAGGATCCAGGGGCCATCAAGGAAAGTGAAGAAGAGATGGAAGAAGATATGGTCACAAAT

Alignment

ORF - retro_tbel_3447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.12 %
• Parental protein coverage: 92.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CLTELILTNNSLLELGD-LDPLASLKSLTYLSILRNPVTNKKHYRLYVIY-KVPQVRVLDFQKVKLKERQ
          C..ELIL.N.SL.ELG..LDPL.SLKSL.YL.ILR....NKKH.RL.V...KV..VRVLD..K.KL....
Retrocopy CVMELILINSSLVELGS<LDPLTSLKSLAYLIILRIAGINKKH*RLHVTV<KVSRVRVLDI*KAKLSF*-

Parental  EAEKMFKGKRGAQLAKDIARRSKTFNPGAGLPTDKKKGGPSPGDVEAIKNAIANASTLAEVERLKGLLQS
          EAEKMFKGK.....AK...RR...FNPG..L..DKKKG.P..G..EAI.NAIANASTLA.VERL...LQ.
Retrocopy EAEKMFKGK---EVAKNFVRRNNMFNPGMELSIDKKKGRPPLGEAEAIENAIANASTLAAVERL---LQN

Parental  GQIPGRERRSGPT-DDGEEEMEEDTVAN
          GQI....R..GP.....EEEMEED.V.N
Retrocopy GQITW-QRIQGPS<KESEEEMEEDMVTN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3447 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3447 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007128	1 retrocopy	retro_amel_850,
Bos taurus	ENSBTAG00000013593	1 retrocopy	retro_btau_1453,
Canis familiaris	ENSCAFG00000010564	1 retrocopy	retro_cfam_1208,
Echinops telfairi	ENSETEG00000010019	1 retrocopy	retro_etel_1366,
Felis catus	ENSFCAG00000018594	1 retrocopy	retro_fcat_322,
Homo sapiens	ENSG00000131876	2 retrocopies	retro_hsap_2148, retro_hsap_2601,
Loxodonta africana	ENSLAFG00000012638	1 retrocopy	retro_lafr_1230,
Myotis lucifugus	ENSMLUG00000014213	1 retrocopy	retro_mluc_2442,
Mustela putorius furo	ENSMPUG00000010938	1 retrocopy	retro_mputfur_1139,
Oryctolagus cuniculus	ENSOCUG00000017417	3 retrocopies	retro_ocun_1248, retro_ocun_1775, retro_ocun_366,
Pan troglodytes	ENSPTRG00000007513	1 retrocopy	retro_ptro_1525,
Tupaia belangeri	ENSTBEG00000001669	2 retrocopies	retro_tbel_1772, retro_tbel_3447 ,
Tarsius syrichta	ENSTSYG00000003965	2 retrocopies	retro_tsyr_1229, retro_tsyr_1943,