RetrogeneDB ID: retro_lafr_74

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:62767232..62768480(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000000424
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HNRNPH1
• Ensembl ID: ENSLAFG00000015766
• Aliases: None
• Description: None

Sequence

>retro_lafr_74
ACGATGCTGGGTCCTGAGGGAGGTGAAGGATTTGTGGTCAAGCTCCGCGGCTTGCCGTGGTCTTGCTCTATTGAGGATGT
GCAGAATTTCCTCTCTGAATGCAAAATTCATGATGGCGTTGCAGGTGTTCATTTCATCTACACCAGAGAAGGCAGACAGA
GTGGTGAGGCTTTTGTTGAACTTGAATCAGAAGAAGATGTAAAAATGGCCCTGAAGAAAGACAGAGAAAGCATGGGGCAT
CGCTATATTGAGGTATTTAAGTCCCACAGAACCGAAATGGATTGGGTGTTGAAGCACAGCGGTCCAAACAGTGCCGACAC
TGCCAATGATGGCTTTGTGCGCCTTCGAGGACTCCCGTTTGGATGCACAAAGGAAGAAATTGTTCAGTTCTTCTCAGGGT
TGGAAATCATGCCGAATGGGATCACTTTGCCGGTGGACCCTGAGGGCAAGATTACAGGGGAAGCCTTCGTGCAGTTTGCC
TCCCAGGAATTAGCTGAGAAGGCTCTAGGGAAGCACAAGGAAAGAATAGGGCATAGGTATATTGAAGTGTTCAAGAGCAG
CCAGGAGGAAGTGAGATCATACTCTGATCCCCCTCTGAAGTTCATGTCTGTGCAGCGGCCAGGGCCCTATGATCGACCCG
GCACTGCCCGGAGATACATTGGCATTGTCAAACAAGCAGGCTTTGACAGGATGAGGTCTGGGGCCTATAGCACAGGCTAT
GGGGGCTATGAAGAGTACAGTGGCCTCAGCGACAGCTATGGCTTTACCACCGATCTGTTTGGAAGAGATCTCAGTTATTG
CCTGTCAGGAATGTATGACCACAGATACGGAGACAGTGAGTTCGCTGTCCAGAGCACAACCGGACACTGTGTCCACATGA
GGGGGCTACCGTACAAAGCAACCGAGAATGACATCTATAACTTCTTCTCTCCACTCAACCCCGTGAGAGTGCATATTGAG
ATTGGCCCTGATGGAAGAGTGACCGGCGAAGCAGATGTCGAGTTTGCCACTCACGAAGAAGCTGTGGCCGCTATGTCAAA
AGACAGAGCCAACATGCAGCACAGATACATAGAGCTCTTCTTGAATTCAACCACAGGGGCCAGCAATGGGGCTTACAGTA
GCCAAATGATGCAGGGCATGGGGGTGTCGACCCAGTCCACGTACACTGGCCTTGAGAGCCAGTCAGTGAGCGGCTGTTAC
GGGGCTGGCTATAGCGGTCAGCAGAACAGCATGGGTGGGTACGACTAG

Alignment

ORF - retro_lafr_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.27 %
• Parental protein coverage: 86.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLGTEGGEGFVVKVRGLPWSCSAEEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDDVKLAL
          MLG.EGGEGFVVK.RGLPWSCS.E.VQ.F.S.CKI..G..G..FIYTREGR.SGEAFVELESE.DVK.AL
Retrocopy MLGPEGGEGFVVKLRGLPWSCSIEDVQNFLSECKIHDGVAGVHFIYTREGRQSGEAFVELESEEDVKMAL

Parental  KKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGI
          KKDRE.MGHRY.EVFKS...EMDWVLKH.GPNS.DTANDGFVRLRGLPFGC.KEEIVQFFSGLEI.PNGI
Retrocopy KKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSADTANDGFVRLRGLPFGCTKEEIVQFFSGLEIMPNGI

Parental  TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPYD
          TLPVD..G..TGEAFVQFASQE.AEKAL.KHKERIGHRYIE.FKSS..EVR...DPP.K.M..QRPGPYD
Retrocopy TLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQEEVRSYSDPPLKFMSVQRPGPYD

Parental  RPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGGS
          RPG..R.Y..I...AGF.RMR.GAY..GYGGY..Y.G..D.YGF..D.FGRDL.YC.SGM.DHRYGD...
Retrocopy RPGTARRYIGIVKQAGFDRMRSGAYSTGYGGYEEYSGLSDSYGFTTDLFGRDLSYCLSGMYDHRYGDSEF

Parental  TFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKAN
          ..QSTTGHCVHMRGLPY.ATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHE.AVAAMSKD.AN
Retrocopy AVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRAN

Parental  MQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMG--GMGLS-NQSSYGG
          MQHRY.ELFLNST.GAS.GAY..........ST.....G.......G..G.G.S..Q.S.GG
Retrocopy MQHRYIELFLNSTTGASNGAYSSQMMQGMGVSTQSTYTGLESQSVSGCYGAGYSGQQNSMGG

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_74 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003841	4 retrocopies	retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Erinaceus europaeus	ENSEEUG00000010991	1 retrocopy	retro_eeur_481,
Erinaceus europaeus	ENSEEUG00000013364	2 retrocopies	retro_eeur_478, retro_eeur_649,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Loxodonta africana	ENSLAFG00000015766	2 retrocopies	retro_lafr_366, retro_lafr_74 ,
Myotis lucifugus	ENSMLUG00000016625	1 retrocopy	retro_mluc_124,
Macaca mulatta	ENSMMUG00000010843	1 retrocopy	retro_mmul_2,
Monodelphis domestica	ENSMODG00000009436	3 retrocopies	retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,