RetrogeneDB ID: retro_lafr_1019

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_6:83652506..83653419(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSLAFG00000001527
• Aliases: None
• Description: Chaperone protein DnaJ A [Source:UniProtKB/TrEMBL;Acc:G3SNQ5]

Sequence

>retro_lafr_1019
TTTGGAGGGGGTGGAAGGATGCAGAGAGAAAGGAGAGGAAAAAACGTGCATCTACTTTCAGTAACATTAGAAGATTTATA
TAAGGGTGCAACGAAAAAACTAGCTCTGCAAAAGAACGTGATTTGTGACAAATGTGAAGGCCAAGGTGTAAAGAAAGGAG
CAGTAGAGTATTGTCCTAATTGCTGAGGTACTGGAATGCACATATGAATCCATCAGGTAGGACCTGGAATGGTTCAGCAA
ACTCAGTTTCTGTCATGGAGTTCCAGGGCCATGGGGAACGAATCAGTCCTAAAGATAGATGTAAAAGTTGCAATGGAAGG
AAGATAGTTCAGGAGAAGAAGATTCTAGAAGTTCACATGGACAAAAGCGTGAAAGATAGTCAGAAGATAACATTCCATGG
TGAAGGAGACCAAGAGCCAGGACTGGAGTCATGCGATATTATCATTGTTTTAAATCAGAAGATACCATGCTGTTTTTGCT
AGATGAGGAGAGGACCTTTTCATGCCTATGGACATATAGCTGGTTGAAGAGTTGTATAACTTCCAAAAGCCAATATCCAC
TCCTGACAACCAAACTATAGTCATCACCTCTCATCAGGATCAAATTGTGAGCATGAAATACCAAGTGTGTGCTAAATGAA
GCCATGCCAATTTATTGTAGACCATATGAAAAGGGTGTCTAATTGTTGAATTTAAGGTAAACTTCCCTGAGAAAGACTTT
CTCTCTTCCGATAAACTCTCGTTGCTGGAAAAACTCCTACCTGAGAGGAAGGAAGTAGAAAGAGACTGATGAAATGGATC
AGGTAGAACTGGTGGACTTTGATCCAAACCAGAAAAGACGATGCCATTACAATGGGGCAGCATAAGAGGAAGGCGACTAT
CTCCACAGAGGTGAGGTTCAGTGTCAGACCTCT

Alignment

ORF - retro_lafr_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.81 %
• Parental protein coverage: 76.69 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  FGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGRGGKKGAVECCPNCRGTGMQIR
          FGGGGRMQRERRGKNV.H.LSVTLEDLY.GAT.KLALQKNVICDKCEG.G.KKGAVE.CPNC.GTGM.I.
Retrocopy FGGGGRMQRERRGKNV-HLLSVTLEDLYKGATKKLALQKNVICDKCEGQGVKKGAVEYCPNC*GTGMHI*

Parental  IHQIGPGMVQQIQSVC-MECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQKITFHGEGDQ
          IHQ.GPGMVQQ.Q....ME.QGHGERISPKDRCKSCNGRKIV.EKKILEVH.DK..KD.QKITFHGEGDQ
Retrocopy IHQVGPGMVQQTQFLS<MEFQGHGERISPKDRCKSCNGRKIVQEKKILEVHMDKSVKDSQKITFHGEGDQ

Parental  EPGLEPGDIIIVLDQK-DHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVITSHPGQIV-KHE
          EPGLE..DIIIVL.QK..HAVF.R.GEDLFM.MDI.LVE.L..FQKPIST.DN.TIVITSH..QIV..HE
Retrocopy EPGLESCDIIIVLNQK>YHAVFAR*GEDLFMPMDI*LVEELYNFQKPISTPDNQTIVITSHQDQIV<EHE

Parental  -DIKCVLNEGMPIYRRPYE-KGRLIIEFKVNFPENGFLSPEKLSLLEKLLPERKEVE-ETDEMDQVELVD
          ...KCVLNE.MPIY.RPYE.KG.LI.EFKVNFPE..FLS..KLSLLEKLLPERKEVE.ETDEMDQVELVD
Retrocopy <NTKCVLNEAMPIYCRPYE<KGCLIVEFKVNFPEKDFLSSDKLSLLEKLLPERKEVE>ETDEMDQVELVD

Parental  FDPNQERRRHYNGEAYEDDDHHPRGGVQCQTS
          FDPNQ.RR.HYNG.A.E..D...RG.VQCQTS
Retrocopy FDPNQKRRCHYNGAA*EEGDYLHRGEVQCQTS

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_1019 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 8 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Loxodonta africana	ENSLAFG00000001527	2 retrocopies	retro_lafr_1019 , retro_lafr_936,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Vicugna pacos	ENSVPAG00000001299	1 retrocopy	retro_vpac_367,