RetrogeneDB ID: retro_lafr_1249

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_96:4022546..4023174(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSAT1
• Ensembl ID: ENSLAFG00000017917
• Aliases: None
• Description: Phosphoserine aminotransferase [Source:UniProtKB/TrEMBL;Acc:G3TJT4]

Sequence

>retro_lafr_1249
TGCACAAACAAGACTGTGCATGGAATGGAGTTCGATTTTATACCTGATGTCAGAGGAGCAGCGTTGGTTTGTGACATGTC
CTCAAGCTTCCTATCCAAGCCAGTGGATGTTTCCAAGCAAGTTTTTGCTGGTGCTCAGAAGAACGTCAGCTCTGCTGGGG
TCATGGTGGTGATCGTCATGATGACTTGCTAGGGTTCACTCTCTGAGAATCCTTCTCCATCCTGGAATACAAAGTGCAAG
CTGGAAACAACTCCTTGTATAACATGCCTCCGTGCTTCAGCATCTATGTCATAGGACTGGTCCTGGAGTAGATTAAGAAC
AATGGCAATGCAACAGCCATGGAGAAGCTTAGCTCCATGAATCTCAAATGATTGATGATATCATTGATAATGCTCAAGGA
TTCTGTGTATGTCCAGTGGAGCCACAGAATAGAAGCAAGATGAATATTCCATTCCACATTGGCAACACCAAAGGAGATGA
TGCTCTAGAAAAAAGATTTGTGGTGAAAGCTCTTGAACTCAACATGGTGTCCTTGAAAGAGCACAGGTCCATGGAAGGCA
TCCATGCCTCTCTGTATAATACTGTCACCATTGAAGATGTTCAGAAGCTGACAGCCTTCATGAAAAAT

Alignment

ORF - retro_lafr_1249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.31 %
• Parental protein coverage: 57.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIV-RDDLLGFA
          C.N.TVHG.EFDFIPDV.GA.LVCDMSS.FLSKPVDVSK....FAGAQKNV.SAGV.VVIV..DDLLGF.
Retrocopy CTNKTVHGMEFDFIPDVRGAALVCDMSSSFLSKPVDVSK--QVFAGAQKNVSSAGVMVVIV<HDDLLGFT

Parental  LQECPSILEYKVQAGNNSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSI-KSEMIYDIIDNSQGFY
          L.E..SILEYKVQAGNNSLYN.PPCFSIYV.GLVLE.IKNNG.A.AMEKLSS...S.MI.DIIDN.QGF.
Retrocopy L*ESFSILEYKVQAGNNSLYNMPPCFSIYVIGLVLE*IKNNGNATAMEKLSSM<ESQMIDDIIDNAQGFC

Parental  VCPVEPQNRSKMNIPFRIGNAKGDDALEKRFVDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAA
          VCPVEPQNRSKMNIPF.IGN.KGDDALEKRFV.KALELNM.SLK.HRS..GI.ASLYN.VTIEDVQKL.A
Retrocopy VCPVEPQNRSKMNIPFHIGNTKGDDALEKRFVVKALELNMVSLKEHRSMEGIHASLYNTVTIEDVQKLTA

Parental  FMKN
          FMKN
Retrocopy FMKN

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_1249 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006898	1 retrocopy	retro_amel_375,
Bos taurus	ENSBTAG00000013960	1 retrocopy	retro_btau_1658,
Canis familiaris	ENSCAFG00000001570	1 retrocopy	retro_cfam_269,
Choloepus hoffmanni	ENSCHOG00000003817	1 retrocopy	retro_chof_2702,
Callithrix jacchus	ENSCJAG00000003319	1 retrocopy	retro_cjac_1203,
Echinops telfairi	ENSETEG00000004158	1 retrocopy	retro_etel_99,
Homo sapiens	ENSG00000135069	3 retrocopies	retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla	ENSGGOG00000015480	1 retrocopy	retro_ggor_407,
Loxodonta africana	ENSLAFG00000017917	2 retrocopies	retro_lafr_1249 , retro_lafr_660,
Macaca mulatta	ENSMMUG00000011868	2 retrocopies	retro_mmul_1029, retro_mmul_2341,
Mustela putorius furo	ENSMPUG00000012566	1 retrocopy	retro_mputfur_808,
Nomascus leucogenys	ENSNLEG00000002989	3 retrocopies	retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus	ENSOCUG00000007765	1 retrocopy	retro_ocun_1092,
Pongo abelii	ENSPPYG00000019313	3 retrocopies	retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes	ENSPTRG00000021045	2 retrocopies	retro_ptro_1606, retro_ptro_316,
Rattus norvegicus	ENSRNOG00000013971	1 retrocopy	retro_rnor_1663,
Tupaia belangeri	ENSTBEG00000012946	1 retrocopy	retro_tbel_1577,
Tarsius syrichta	ENSTSYG00000000093	2 retrocopies	retro_tsyr_1073, retro_tsyr_1212,