RetrogeneDB ID: retro_lafr_1230

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:26462298..26462876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPA1
• Ensembl ID: ENSLAFG00000012638
• Aliases: None
• Description: None

Sequence

>retro_lafr_1230
GTAGCGCTGACGGCGGAGCTGATCCAGCCCACGGCGCAGTACACCAACGCCATGCCAGATGACAGCTGGACCTCCGGGGT
TATAAAATTCCTGTCATTGAAAATCTAGGTGTTACCTTAGACCAGTTTGATGCTATTGATTTTTCTAACAATGAAATCAG
GAAACTGGATGGTTTTCCTCTGTTGTGAAGACTGAAAACATTATTGGTGAGCAATCACAGAATATGCCATATAGGTAAGG
GATTTAATCTGTCTCTACCCTGTTTGACAGAACTCATTCTCATCAACAACAGTCTTGTGGAACTGGGTGATCTGGACCCT
TTGGCAGCTCTCCAATCACTGACTTATTTAAGTATTCTAAGGAATCCTGTAACAGATAAGAAGCATTACAGACTGTATGT
AATTTACAAAGTTCCACAAGTCAGAGTACTGGCTTTCCAGAAACAGTAACAAAAAGTGCATCAGGAAGCAGAGAAAATGT
TCAAGGGCAAACAAGGTGCACAACTTAAAAAGGATATTACCAGGAGAAGCAAAACTTTTCATCCAGGTGCTGGTTGGCCA
ACTGACAGAAAGGTGGGC

Alignment

ORF - retro_lafr_1230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.9 %
• Parental protein coverage: 75.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKLNGELIEQAAQY-NAVRTASW-NLRGYKIPVIENLGATLDQFDAIDFSDNEIRKLDGFPLLRRLKTLL
          V.L..ELI...AQY.NA....SW..LRGYKIPVIENLG.TLDQFDAIDFS.NEIRKLDGFPLL.RLKTLL
Retrocopy VALTAELIQPTAQYTNAMPDDSW<DLRGYKIPVIENLGVTLDQFDAIDFSNNEIRKLDGFPLL*RLKTLL

Parental  VNNNRICRIGEGLDQSLPCLTELILTNNSLVELGDLDPLAALKSLTYLSILRNPVTNKKHYRLYVIYKVP
          V.N.RIC.IG.G...SLPCLTELIL.NNSLVELGDLDPLAAL.SLTYLSILRNPVT.KKHYRLYVIYKVP
Retrocopy VSNHRICHIGKGFNLSLPCLTELILINNSLVELGDLDPLAALQSLTYLSILRNPVTDKKHYRLYVIYKVP

Parental  QVRVLDFQKVKLKERQEAEKMFKGKRGAQLAKDIARRSKTFNPGAGLPTDKKKG
          QVRVL.FQK...K..QEAEKMFKGK.GAQL.KDI.RRSKTF.PGAG.PTD.K.G
Retrocopy QVRVLAFQKQ*QKVHQEAEKMFKGKQGAQLKKDITRRSKTFHPGAGWPTDRKVG

Legend:

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

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_1230 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana 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,