RetrogeneDB ID: retro_lafr_366

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_130:1817162..1818221(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000017391
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_lafr_366
ATGATGCTGAGCACAGAAGGCAGGGAGGGGTTCGTGGTGAAGGTCAGGGGCCTACCCTGGTCCTGCTCAGCCGATGAGGT
GATGCGCTTCTTCTCTGATTGCAAAATCCAAAATGGCACATCAGGTATCCGTTTTATCTACACCAGAGAAGGCAGACCAA
GCGGTGAAGCATTTGTCGAACTTGAATCCGAAGATGAAGTGAAACTGGCTTTGAAGAAGGACAGAGAAACCATGGGACAC
AGATACGTGGAAGTATTCAAGTCCAACAGCGTTGAAATGGATTGGGTGTTGAAGCATACAGGTCCGAATAGCCCTGATAC
TGCCAATGATGGCTTCGTCCGGCTTAGAGGACTCCCATTTGGCTGTAGCAAGGAAGAAATTGTTCAGTTCTTTTCAGGGT
TGGAAATTGTGCCAAATGGGATGACACTGCCGGTGGACTTTCAGGGGCGGAGCACAGGGGAGGCCTTTGTGCAGTTTGCT
TCGCAGGAGATAGCTGAAAAGGCCTTAAAGAAACACAAGGAAAGAATAGGGCACAGGTACATTGAAATCTTCAAGAGTAG
CCGAGCTGAAGTCCGAACCCACTATGATCCTCCTCGAAAGCTCATGGCTATGCAGCGGCCAGGTCCCTATGATAGGCCAG
GGGCCGGCAGAGGGTATAATAGCATTGGCAGAGGAGCTGGGTTTGAAAGGATGAGGCGGGGTGCCTATGGTGGAGGGTAT
GGAGGGTATGATGACTATGGTGGCTATAATGATGGGTATGGCTTTGGGTCTGATAGATTTGGAAGAGACCTCAATTACTG
TTTTTCAGGAATGTCTGATCATAGATATGGAGATGGTGGGTCCAGTTTCCAGAGCACCACAGGGCACTGTGTACACATGA
GGGGGTTACCTTACAGAGCCACTGAGAATGATATTTACAATTTTTTCTCCCCTCTTAACCCTATGAGAGTACACATTGAA
ATTGGACCTGATGGCAGAGTTACTGGTGAGGCAGATGTTGAATTTGCTACTCATGAAGATGCTGTGGCAGCTATGGCAAA
AGACAAAGCTAATATGCAA

Alignment

ORF - retro_lafr_366 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.05 %
• Parental protein coverage: 78.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMLGTEGGEGFVVKVRGLPWSCSAEEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDDVKLA
          MML.TEG.EGFVVKVRGLPWSCSA.EV.RFFSDCKIQNG..GIRFIYTREGRPSGEAFVELESED.VKLA
Retrocopy MMLSTEGREGFVVKVRGLPWSCSADEVMRFFSDCKIQNGTSGIRFIYTREGRPSGEAFVELESEDEVKLA

Parental  LKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
          LKKDRETMGHRYVEVFKSN.VEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
Retrocopy LKKDRETMGHRYVEVFKSNSVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG

Parental  ITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
          .TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
Retrocopy MTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY

Parental  DRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
          DRPGAGRGYNSIGRGAGFERMRRGAY........DY.GYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
Retrocopy DRPGAGRGYNSIGRGAGFERMRRGAYXXXXXXXXDYGGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG

Parental  STFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKA
          S.FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP.RVHIEIGPDGRVTGEADVEFATHEDAVAAM.KDKA
Retrocopy SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKA

Parental  NMQ
          NMQ
Retrocopy NMQ

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_366 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,