RetrogeneDB ID: retro_lafr_941

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_5:66782760..66784037(-)
• Located in intron of: ENSLAFG00000005331

Retrocopy information

• Ensembl ID: ENSLAFG00000027017
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000001563
• Aliases: None
• Description: None

Sequence

>retro_lafr_941
ATGCCCCCCAAGAAACAGGCTCAGGCCGGGGGCAGCAAAAAGGCGGAGCAGAAAAAGAAGGAGAAGATCATCGAAGACAA
AACTTTTGGTCTAAAGAATAAGAAAGGAGCAAAGCAACAGAAGTTTATCAAGGCTGTCACTCATCAAGTTAAATTTGGTC
AACAAAATCCACGTCAGGTAGCACAAAGTGAAGCTGAAAAGAAATTGAAGAAGGATGACAAGAAGAAGGAATTGCAGGAG
CTAAATGAACTATTCAAACCTGTAGTTGCTGCTCAAAAAATAAGTAAAGGTGCAGATCCCAAGTCCGTGGTATGTGCATT
CTTCAAGCAAGGACAGTGTTCCAAAGGAGATAAGTGTAAGTTCTCTCATGACTTGACTCTGGAGAGAAAATGTGAAAAGC
AAAGTGTTTACATTGACACAAGAGATGAAGAACTTGAAAAAGATACCATGGATAATTGGGATGAAAAAAAACTGGAAGAA
GTAGTGAACAAGAAGCACGGTGAGGCGGAAAAGAAAAAACCAAAAACTCAAATAGTATGCAAGCATTTCCTTGAAGCTAT
TGAAAACAACAATATGGCTGGTTTTGGGTATGCCCTGGAGGGGGTGATATGTGCATGTATCGTCATGCACTTCCTCCTGG
ATTTGTGTTGAAAAAAGATAAAAAGAAAGAAGAGAAAGAAGACGAAATTTCATTAGAAGACCTCATTGAAAGAGAGCGTT
CTGCCCTAGGTCCAAATGTTACCAAAATCACTCTAGAATCTTTTCTTGCATGGAAAAAAAGGAAAAGACAAGAAAAGATT
GATAAACTTGAGCAAGATATGGAAAGAAGGAAAGCAGACTTCAAAGCAGGGAAAGCACTAGTGATCAGTGGTCGTGAGGT
GTTTGAATTTCGTCCTGAACTGGTCGATGATGATGATGAGGAAGCAGATGATACCCATTACATGCAGGGAACAGGTGGTG
ATGAGGTTGATGATTCTGTGAGCATAAATGACATAGATTTAAGCCTGTACATTCCAAGAGATGTAGATGAGACAGGTATT
ACTGTAGCCAGTCTTGAAAGATTCAGCACGTACACTTCAGAAAAAGATGAAAACAAATTAAGTGAAGCTTCTGGAGGTAG
GGCTGAAAATGGGGAAAGGAGTGACCTGGAAGAGGACAACGAAGGGGAGGAACAGGAAAATGGAGCCATCGACGCTGTTC
CTGTTGATGAAAACCTTTTCACTGGGGAAGATTTGGATGAACTAGAAGAAGAATTAAACACACTTGATTTAGAAGAA

Alignment

ORF - retro_lafr_941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
          MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
Retrocopy MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK

Parental  KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCSKGDKCKFSHDLTLERKCEKRSVYIDA
          KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCSKGDKCKFSHDLTLERKCEK.SVYID.
Retrocopy KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCSKGDKCKFSHDLTLERKCEKQSVYIDT

Parental  RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENN-KYGWFWVCPGGGDMCMYRH
          RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENN..YGWFWVCPGGGDMCMYRH
Retrocopy RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENN<QYGWFWVCPGGGDMCMYRH

Parental  ALPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKA
          ALPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKA
Retrocopy ALPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERRKA

Parental  DFKAGKALVISGREVFEFRPELVDDDDEEADDTRYTQGTGGDEVDDSVSINDIDLSLYIPRDVDETGITV
          DFKAGKALVISGREVFEFRPELVDDDDEEADDT.Y.QGTGGDEVDDSVSINDIDLSLYIPRDVDETGITV
Retrocopy DFKAGKALVISGREVFEFRPELVDDDDEEADDTHYMQGTGGDEVDDSVSINDIDLSLYIPRDVDETGITV

Parental  ASLERFSTYTSEKDENKLSEASGGRAENGERSDLEEDNEGEEQENGAIDAVPVDENLFTGEDLDELEEEL
          ASLERFSTYTSEKDENKLSEASGGRAENGERSDLEEDNEGEEQENGAIDAVPVDENLFTGEDLDELEEEL
Retrocopy ASLERFSTYTSEKDENKLSEASGGRAENGERSDLEEDNEGEEQENGAIDAVPVDENLFTGEDLDELEEEL

Parental  NTLDLEE
          NTLDLEE
Retrocopy NTLDLEE

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_941 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 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941 ,
Myotis lucifugus	ENSMLUG00000007741	2 retrocopies	retro_mluc_1494, retro_mluc_2467,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,