RetrogeneDB ID: retro_lafr_809

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_4:35193109..35194500(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSLAFG00000026567
• Aliases: None
• Description: None

Sequence

>retro_lafr_809
ATGGAAACTGAACAGCCAGAGGAAACCTTTCCCAACACTGAAACCAAGGGTGAATTGGGTAAACGCCCTGCAGAAGGTAT
GGCAGAGGAACAAGCGTTTAAAAGATCTAGGAACCTGATGAAATGGTTGAGCTGCTCATTCTGCTTCAGAGCAAGAATGC
TGGGGCAGTGGTTGGAAAAGGAGGCAAAAATATTAAGGCTTTTCGTACAGAGTACAACGACAGTGTTTCAGTCCCAGACA
GCAGTGGCCTCGAGCGCATGTTGAGTATCAGTGCTGATATTGAAACAATTGGAGAAATTCTGAAGAAAACCATCCCTACC
TTGGAAGAGGGACTGAAGTTGCCATCACCCACTGCAACCAGCCAGCTCCGGCTCGAATCTGATGCTGTGGAATGCTTAAA
TTACCAACACTATAAAGGAAGCGAGTTTGACTGCGAGTTGAGACTGTTGATTCATCAGAGTCTGGCGGGAGGAATTATTG
GGGTCAAAGATGCTAAAATCAAAGAACTCCGAGAGAACACTCAGACAACAATCAAGCTTTTCCAGGAATGCTGGACTCTT
TCCACTGACAGAGTCGTTCTTATTGGAGGAAAGCCAGATAGGGTCGTAGAGTGCATAAAAATCATCCATGATCTTATATC
TGAGTTGCCCATCAAAGGACGTGCACAGCCTTATGATGCCAATCTTTAAGATGAAACCTATAATTATGGTGGCTTTACAA
TGATGTTTGATGACCGGCGTGGACATCCCGTGGGATTCCCTATGCTGGGAAGAGGTGGTTTTGACAGAATGGCTCCTGGT
CGGAGTGGACGTCCCATGCCTCCTTCTAGAAGAGGTTATGACGACATGAGCCCTCATCTAGGACCTCCTCCTCCTCCTCC
TGGACGAGGTGGCCGGGGTGGTAGCAGAGCTCGGAATCTTCCTCTTCCTCCACCACCACCACCTAGAGGAGGAGATCTAA
TAGCTTATGACAGAAGAGGGAGACCTGGAGACCGTTACCATGGCATGGTTGGTTTCAGTGCTGATGAAACTTGGGATTCT
GCAACAGATACATGGTGACCATCAGAGTGGCAGATGGCTTATGAACCACACGGTGGCTCCGGATATGATTATTCCTATGC
AGGGGGTCATGGCTCACATGGTGATCTTGGTGGACCTATCATTACCACACAAGTAACTATTCCCAAAGATTTGGCTGAAT
CTATTATTGGCAAAGGTGGTCAGCGGATTAAACAAATCCGTCATGAGTCTGGAGCTTCAATCAAAATTGATGAACCTTTA
GAAGGATCCGAAGATCGGATCATTACCATCACAGGAACACAGGACCAGACACAGAATGCACAGTGTCTGCTGCAGAACCG
TGTGAAGCAGTATGCAGATGTTGAAGGATTC

Alignment

ORF - retro_lafr_809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  METEQPEETFPNTETNGEFGKRPAEDMEEEQAFKRSRNT-DEMVELRILLQSKNAGAVIGKGGKNIKALR
          METEQPEETFPNTET.GE.GKRPAE.M.EEQAFKRSRN..DEMVEL.ILLQSKNAGAV.GKGGKNIKA.R
Retrocopy METEQPEETFPNTETKGELGKRPAEGMAEEQAFKRSRNL<DEMVELLILLQSKNAGAVVGKGGKNIKAFR

Parental  TDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK
          T.YN.SVSVPDSSG.ER.LSISADIETIGEILKK.IPTLEEGL.LPSPTATSQL.LESDAVECLNYQHYK
Retrocopy TEYNDSVSVPDSSGLERMLSISADIETIGEILKKTIPTLEEGLKLPSPTATSQLRLESDAVECLNYQHYK

Parental  GSDFDCELRLLIHQSLAGGIIG-KGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKII
          GS.FDCELRLLIHQSLAGGIIG.K.AKIKELRENTQTTIKLFQEC...STDRVVLIGGKPDRVVECIKII
Retrocopy GSEFDCELRLLIHQSLAGGIIGVKDAKIKELRENTQTTIKLFQECWTLSTDRVVLIGGKPDRVVECIKII

Parental  LDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRRD
          .DLISE.PIKGRAQPYD.N..DETY.YGGFTMMFDDRRG.PVGFPM.GRGGFDRM.PGR.GRPMPPSRR.
Retrocopy HDLISELPIKGRAQPYDANL*DETYNYGGFTMMFDDRRGHPVGFPMLGRGGFDRMAPGRSGRPMPPSRRG

Parental  YDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDGMVGFSADETWDSAI
          YDDMSP..GPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDL.AYDRRGRPGDRY.GMVGFSADETWDSA.
Retrocopy YDDMSPHLGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLIAYDRRGRPGDRYHGMVGFSADETWDSAT

Parental  DTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGA
          DTW.PSEWQMAYEP.GGSGYDYSYAGG.GS.GDLGGPIITTQVTIPKDLA.SIIGKGGQRIKQIRHESGA
Retrocopy DTW*PSEWQMAYEPHGGSGYDYSYAGGHGSHGDLGGPIITTQVTIPKDLAESIIGKGGQRIKQIRHESGA

Parental  SIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYADVEGF
          SIKIDEPLEGSEDRIITITGTQDQ.QNAQ.LLQN.VKQYADVEGF
Retrocopy SIKIDEPLEGSEDRIITITGTQDQTQNAQCLLQNRVKQYADVEGF

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_809 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809 ,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,