RetrogeneDB ID: retro_lafr_650

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_28:15451138..15451897(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRPDL
• Ensembl ID: ENSLAFG00000008612
• Aliases: None
• Description: None

Sequence

>retro_lafr_650
CATTTGTCTCGATTTGGAGAGGTTGTAGACTGCACAGTTAAAACAGATCTGGTCACTGGACGGTCAAGAGGATTTGGATT
TGTGCGTTTCAAAGACGCTGCTAGTGTTGGTAAGATTTTGGAACTGAAAGAACACAAACTGGATGCCAAATTGACAGACC
CCAAAAGGGCCAAAGCTTCAAAAAGGAAGGAACCTCCCAAAAAGGTTTTTGTGGGTGGATTGAGCCCAGATTCTTCTGAA
GAACAACTTAAAGAATGTTTTGGCGCTTTCAGAGAGGTTGAAAATACTGAATTTCCCGTGGATACAAAAACAAATGAAAG
AAAAGGATTTTGTTTTATCACATATACAGATGAAGAGCCCGTAAAGGAATTATAAGAAAGCAGATACCATCAAATTGGTT
CTGGGAAGTGTGAAATCAAAGTTGCACAACCCAAAGAGGTATATAGGCAGCAACAGCAGAAAGGAGGAAGAGGTGCCACA
GCTGGTGGGCGAGGTGGTACTCGGGGTCGGGGTCGAGGTCAGGGCCAAAACTGGAACCAAGGATTTAATGACTTTTTATG
ACCAAGGATACGGGAAATTACAGTAGTGCCTATGGTGGTGATTAAAACTGTAGTGGCTATGGGCGGATATGATTATACTG
GGTAGAACTATGGGAACTATGGATGTGGACAGGAATATGCAGACTACAGTGGCCAACAGAGCACATATGGCAGGGCATCT
CGAGTGGGTGGCAATCACCAAAACAATTACCAGCCATAC

Alignment

ORF - retro_lafr_650 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.99 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKEPPKKVF
          .LSRFGEVVDCT.KTD.VTGRSRGFGFV.FKDAASV.K.LELKEHKLD.KL.DPKRAKA.K.KEPPKKVF
Retrocopy HLSRFGEVVDCTVKTDLVTGRSRGFGFVRFKDAASVGKILELKEHKLDAKLTDPKRAKASKRKEPPKKVF

Parental  VGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGSGKCEIK
          VGGLSPD.SEEQ.KE.FGAF.E.EN.E.P.DTKTNER.GFCFITYTDEEPVK.L.ESRYHQIGSGKCEIK
Retrocopy VGGLSPDSSEEQLKECFGAFREVENTEFPVDTKTNERKGFCFITYTDEEPVKEL*ESRYHQIGSGKCEIK

Parental  VAQPKEVYRQQQQQQKGGRGATAGGRGGTRGRGRGQGQNWNQGFNN-YYDQGY-GNYNSAYGGDQNYSGY
          VAQPKEVYRQQQQ..KGGRGATAGGRGGTRGRGRGQGQNWNQGFN...YDQGY.GNY.SAYGGD.N.SGY
Retrocopy VAQPKEVYRQQQQ--KGGRGATAGGRGGTRGRGRGQGQNWNQGFND>FYDQGY>GNYSSAYGGD*NCSGY

Parental  -GGYDYTGYNYGNYGYGQGYADYSGQQSTYGKASRGGGNHQNNYQPY
          .GGYDYTG.NYGNYG.GQ.YADYSGQQSTYG.ASR.GGNHQNNYQPY
Retrocopy >GGYDYTG*NYGNYGCGQEYADYSGQQSTYGRASRVGGNHQNNYQPY

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_650 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008940	1 retrocopy	retro_cfam_1086,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Dipodomys ordii	ENSDORG00000000968	1 retrocopy	retro_dord_145,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650 ,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Loxodonta africana	ENSLAFG00000029587	5 retrocopies	retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Nomascus leucogenys	ENSNLEG00000008636	1 retrocopy	retro_nleu_673,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,