RetrogeneDB ID: retro_lafr_364

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_130:1430148..1431170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSL1D1
• Ensembl ID: ENSLAFG00000013664
• Aliases: None
• Description: None

Sequence

>retro_lafr_364
GGGAGGAGTTAGCTTGCTCTTTCCCCGTGTTCCACTGCACGAGGTGAGGGCGGTAGGAAGGACTCGGCTTTGACCCCAAC
CTCAGCCTCGGCTCAGCGACCCTTGCTGCAGCAGAGCCGCGGCAGGAGCTGGACAAAATACAGGTTAAAAAAGCAGTGAA
GGCTCTGTTGGTGCATTGACAGTCCAGAAAAACACGCTAATGAAGTGCTTTTAAATGAGAATGAAAATTTATTTTTGATG
GCGGTGGTATGGAAAATTCCAAAGAAAGAACTCAGGGTCAGATTATCCTTGCCTTACGGTATTCGATCAGATTTAGCAGA
AATCTGTTTATTTACCAATGACGAGTCCAATTTAACTCCTGAGAAGATGGAACATTTCTATAGGAATATTTTGAAAAAGC
ATAAAATTAAAATCATTTTTCAGGTTATCCTATTCTGAACTTAAAAAAAAAAGAATATAAACCCTATGAAGCCAAGCTCT
GCCTCTTGGGTAGTTTTTACTTCTTCCTTACTGATACAAGTATTAGGAGGCTTTTACCCTCAATTATAGGGAAACATTTC
TATCTCTGAAAGAAAGTCCCAGTATGTGTAAACCTCCTGGCCAAGGATTTATTAAAAAGAAATCAATGACTGTCTTGGTG
GAACTATCATGAACATCTCTAAAAATGGCTCTTGGAGCATATCTGCATTGGTCACACTGGAATGCTGATCCAGCACATTG
TTGAAAATGTCGTTGCTGTCACAAAAGGGCTTTCAGAAAAATAGCCAGAGAAGTGGGGAGTGTGAAACTCTTAGACCTGA
AAACTGAGAAAGCAGTTGCCCTTCCAATCTTTTCTTTGTTCATCAGTGCTTTTTGTGAAGGGAAAGGAGGACCTCTTCCC
GGCCAGAAGAAAAAAGAGGCAAAGAAAAAGCAAAAAGAAAAGCTCCAAAAAAAGGAGAAAAAGGGAAATGCAACAGGCTG
CAAAGACTAAATCAGCCCAAACTAAAGACAAAGTGGCAGCTGAAGTCAATGGTGCTCCAGCA

Alignment

ORF - retro_lafr_364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.5 %
• Parental protein coverage: 72.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GRSYPGGSARSSARGEGGMEASASTPASASPP-ATPAAADPRLELSKTQVKKAVKALLAHSQSRK-NANE
          GRS....S..S.ARGEGG...SA.TP.SAS...AT.AAA.PR.EL.K.QVKKAVKALL.H.QSRK..ANE
Retrocopy GRS*LALSPCSTARGEGGRKDSALTPTSASAQ<ATLAAAEPRQELDKIQVKKAVKALLVH*QSRK>HANE

Parental  VLLNENETLFLMVVLWKIPKKELRVRLSLPYAIRSDLAEVCLFTKDEPNLTPEKTEHFYRNLLNKHKIKT
          VLLNENE.LFLM.V.WKIPKKELRVRLSLPY.IRSDLAE.CLFT.DE.NLTPEK.EHFYRN.L.KHKIK.
Retrocopy VLLNENENLFLMAVVWKIPKKELRVRLSLPYGIRSDLAEICLFTNDESNLTPEKMEHFYRNILKKHKIKI

Parental  ISQII-PLRTLKK-EYKPYEAKLRLLGSFDFFLTDARIRRLLPSIIGKHFYLRKKVPVCVNLLAKDLSK-
          I.Q.I.P...LKK.EYKPYEAKL.LLGSF.FFLTD..IRRLLPSIIGKHFYL.KKVPVCVNLLAKDL.K.
Retrocopy IFQVI<PILNLKKKEYKPYEAKLCLLGSFYFFLTDTSIRRLLPSIIGKHFYL*KKVPVCVNLLAKDLLK>

Parental  EINDCIGGTVMNISKNGSCST-IRVGHTGMMVQHIVENIVAVTKGLSEKLPEKWK-SVKLLYLKTEKSVA
          EINDC.GGT.MNISKNGS.S..I..GHTGM..QHIVEN.VAVTKGLSEK.PEKW..SVKLL.LKTEK.VA
Retrocopy EINDCLGGTIMNISKNGSWSI<ICIGHTGMLIQHIVENVVAVTKGLSEK*PEKWG<SVKLLDLKTEKAVA

Parental  LPIFSSFVSAFYEGEGGPLPGQK-KKFKQKFYRHLLIQTEVLVLQQAAKTKKTKSAQNEDKAAAEVSGAP
          LPIFS.F.SAF.EG.GGPLPGQK.KK...K..............QQAA...KTKSAQ..DK.AAEV.GAP
Retrocopy LPIFSLFISAFCEGKGGPLPGQK>KKRQRKSKKKSSKKRRKREMQQAA---KTKSAQTKDKVAAEVNGAP

Parental  A
          A
Retrocopy A

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_364 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018865	2 retrocopies	retro_cfam_1937, retro_cfam_691,
Choloepus hoffmanni	ENSCHOG00000010827	2 retrocopies	retro_chof_1617, retro_chof_852,
Callithrix jacchus	ENSCJAG00000008375	1 retrocopy	retro_cjac_2154,
Cavia porcellus	ENSCPOG00000010630	3 retrocopies	retro_cpor_1262, retro_cpor_276, retro_cpor_822,
Loxodonta africana	ENSLAFG00000013664	1 retrocopy	retro_lafr_364 ,
Myotis lucifugus	ENSMLUG00000000784	1 retrocopy	retro_mluc_1309,
Monodelphis domestica	ENSMODG00000029494	2 retrocopies	retro_mdom_1240, retro_mdom_573,
Otolemur garnettii	ENSOGAG00000015151	1 retrocopy	retro_ogar_2604,
Rattus norvegicus	ENSRNOG00000048608	1 retrocopy	retro_rnor_2771,
Sarcophilus harrisii	ENSSHAG00000016705	1 retrocopy	retro_shar_836,