RetrogeneDB ID: retro_lafr_936

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:41097440..41098624(-)
• 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_936
ATGGTGAAAGAAACCACTTACTATGATGTTTTGGGGGTCAAACCCAATGCCACCCAGGAAGAGCTGAAAAAAGCTTATAG
GAAACTGGCCTTGAAGTACCACCCTGATAAGAATCCAAATGAAGGCGAGAAGTTCAAACAAATTTCTCAAGCTTATGAAG
TGCTTTCTGATGCAAAGAAAAGAGAATTGTATGACAAAGGAGGAGAGCAGGCCATCAAAGAGGGTGGAGCAGGTGGTGGT
TTTGGCTCCCCCATGGACATCTTTGATATGTTTTTTGGAGGTGGTGGAAGGATGCAGAGAGAAAGGAGAGGAAAAAATGT
TGTGCGTCAACTGTCAGTGATGTTAGAAGACTTATATAATTGTGCAACAAGAAAACTAGCTCTGCAAAAGAATGTGATTT
GTAGTAAATGTGAAGGCCGAGGTGGTAAGGAGCAGTAGAGTGCTGTCCTAATTGCCGAGGTACTGGAATGTAAATACGAA
TTCATCAGATAGGACCTGGAATGGTTCAGCAAATTCAGTCTGTGCGCATGGAATGCCAGGGCCATGGAGAACAGATCAGC
CCTAAAGACAGATGTAAAAGTTGCAATGGAAGGAAGATCGTTTGAGAGAAGAAGATTCTAGAAGTTCACATTGCCAAAGG
CATGAAAGATGGCCAGAAGATAACATTCCATGGTGAAGGAGACCAAGAGCCAGGACTGGAGCCAGGAGATATTATCATTG
CTTTAGATCAGAAGGACCATGTTGTTTTTACTAGACGAGAAGACCTTTTCATGTGTATGGACATACAGCTGGTTGAGGCA
TTGTGTGGCTTCCAGAAGCCAATATCTACTCTTGACAACCGAACCATAGTCATCACTTCTCATCCAGGTCAGATTGTCAA
GCATGAAGATATCAAGTGTGTGCTAAATGAAGGCATGCCACTTTATCTTAGACCATACGAAAAGGGGCGCCTGATCATCG
AATTTAAGGTAAACTTTCCTGAGAATGGCTTTCTCTCTCCCGAAAAACTCTCTTTGCTGGAAAAACTCCTACCTGAGAGG
AAGGAAGTAGAAGAGACTGATGAAATGGATCAGGTAGAACTGGTGGACTTTGATCCAAACCAGGAAAGACGGCTTCATTA
CAATGGAGAAGCATATGAAGATGATGACCATCACCCCAGAGGTGGGGTTCAGTGTCAGACCTCT

Alignment

ORF - retro_lafr_936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKKQFKQISQAYEVLSDAKKRELYDKGG
          MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEK..FKQISQAYEVLSDAKKRELYDKGG
Retrocopy MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEK--FKQISQAYEVLSDAKKRELYDKGG

Parental  EQAIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCE
          EQAIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVV.QLSV.LEDLYN.ATRKLALQKNVIC.KCE
Retrocopy EQAIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVRQLSVMLEDLYNCATRKLALQKNVICSKCE

Parental  GRGGKK-GAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKI
          GR.G.K.GAVECCPNCRGTGM.IRIHQIGPGMVQQIQSV.MECQGHGE.ISPKDRCKSCNGRKIV.EKKI
Retrocopy GR-GGK<GAVECCPNCRGTGM*IRIHQIGPGMVQQIQSVRMECQGHGEQISPKDRCKSCNGRKIV*EKKI

Parental  LEVHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPI
          LEVHI.KGMKDGQKITFHGEGDQEPGLEPGDIII.LDQKDH.VFTRR.EDLFMCMDIQLVEALCGFQKPI
Retrocopy LEVHIAKGMKDGQKITFHGEGDQEPGLEPGDIIIALDQKDHVVFTRR-EDLFMCMDIQLVEALCGFQKPI

Parental  STLDNRTIVITSHPGQIVKHEDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPEKLSLLEKLLP
          STLDNRTIVITSHPGQIVKHEDIKCVLNEGMP.Y.RPYEKGRLIIEFKVNFPENGFLSPEKLSLLEKLLP
Retrocopy STLDNRTIVITSHPGQIVKHEDIKCVLNEGMPLYLRPYEKGRLIIEFKVNFPENGFLSPEKLSLLEKLLP

Parental  ERKEVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDDHHPRGGVQCQTS
          ERKEVEETDEMDQVELVDFDPNQERR.HYNGEAYEDDDHHPRGGVQCQTS
Retrocopy ERKEVEETDEMDQVELVDFDPNQERRLHYNGEAYEDDDHHPRGGVQCQTS

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_936 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,