RetrogeneDB ID: retro_lafr_585

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:10351723..10352102(+)
• Located in intron of: ENSLAFG00000000845

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC7
• Ensembl ID: ENSLAFG00000001987
• Aliases: None
• Description: None

Sequence

>retro_lafr_585
ATATGCAAATACCTCTTAATTGACAAAGATGGGGCTAGAAATGACTGAATAATTAATGTATTAGTGGAGAATTTCATTAA
GTGATGGAATGCTGGATGTGAGGATGGTCATAACCAGTATCAACAACTGCTGAACACACTGTCACAATGTGAATTTCCAG
TATGGAAAAAAAGTGCATGTATATAATCTGAACCTTACAGAGATGGAAAATTCTGAAAAAAAATCTTAAAACAGGGTGTT
TAGTGTAGCTAACGGTCAGAAAAAAGTTATTGAGTGTAAAAATCAGATTCATCAAGCAAAATGAAGACAAATAAATTGCC
AACAATATGTTTTAGCAGAAGAAATAAAGCTAATTCCAGACATGCAGGTGGCTTTAAAG

Alignment

ORF - retro_lafr_585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.39 %
• Parental protein coverage: 62.75 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRKRLLIDGDGAGDDRRINLLVKSFIKWCNSGSQEEGYSQYQRMLSTLSQCEFSM-GKTLLVYDMNLREM
          I.K.LLID.DGA..D..IN.LV..FIK..N.G..E.G..QYQ..L.TLSQCEF...GK...VY..NL.EM
Retrocopy ICKYLLIDKDGARND*IINVLVENFIK*WNAGC-EDGHNQYQQLLNTLSQCEFPV>GKKVHVYNLNLTEM

Parental  ENYEKIYKEIECSIAGAHEKIAECKKQILQAKRIRKNRQEYDALAKVIQHHPDRHETLK
          EN.EK.......S.A....K..ECK.QI.QAK....N.Q.Y..LA..I...PD....LK
Retrocopy ENSEKKS*NRVFSVANGQKKVIECKNQIHQAK*RQINCQQY-VLAEEIKLIPDMQVALK

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_585 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 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012170	2 retrocopies	retro_chof_2655, retro_chof_722,
Callithrix jacchus	ENSCJAG00000034899	2 retrocopies	retro_cjac_354, retro_cjac_398,
Cavia porcellus	ENSCPOG00000007930	2 retrocopies	retro_cpor_1127, retro_cpor_1164,
Dasypus novemcinctus	ENSDNOG00000005917	5 retrocopies	retro_dnov_2083, retro_dnov_2129, retro_dnov_2335, retro_dnov_2374, retro_dnov_380,
Loxodonta africana	ENSLAFG00000001987	2 retrocopies	retro_lafr_585 , retro_lafr_774,
Myotis lucifugus	ENSMLUG00000012060	1 retrocopy	retro_mluc_369,
Oryctolagus cuniculus	ENSOCUG00000021860	1 retrocopy	retro_ocun_124,
Otolemur garnettii	ENSOGAG00000024865	1 retrocopy	retro_ogar_2733,
Sorex araneus	ENSSARG00000013894	1 retrocopy	retro_sara_41,
Sus scrofa	ENSSSCG00000011491	1 retrocopy	retro_sscr_1182,
Tupaia belangeri	ENSTBEG00000007069	1 retrocopy	retro_tbel_49,
Tursiops truncatus	ENSTTRG00000013618	3 retrocopies	retro_ttru_1365, retro_ttru_23, retro_ttru_957,
Vicugna pacos	ENSVPAG00000010083	1 retrocopy	retro_vpac_68,