RetrogeneDB ID: retro_lafr_294

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_110:893982..895807(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000026615
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF4B
• Ensembl ID: ENSLAFG00000009534
• Aliases: None
• Description: None

Sequence

>retro_lafr_294
TCAGCAAAAAAGAAGAATAAGAAGGGGAAGACTATCTCCCTAACAGATTTCCTGGCTGAGGATGGGGGGACTGGTGGAGG
AAGCACCTATGTCCCCAAACCAGTCAGCTGGGCTGATGAAACAGATGACCTGGAAGGAGATGTTTCAACCACTTGGCACA
GTAACGATGATGACGTGTATAGGGCACCTCCAATTGACCATTCTATCCTGCCCACTGCTCCACGGGCTGCTCGAGAACCC
AATATCGACCGGAGCCGTCTTCCCAAATCACCACCCTACACTGCTTTTCTAGGGAATCTGCCCTACGATGTGACAGAAGA
CTCCATTAAGGAATTCTTTAGAGGATTAAATATCAGTGCAGTGCGCTTACCACGTGAACCCAGCAACCCAGAGAGATTAA
AAGGTTTTGGTTACGCTGAGTTTGAGGACCTGGATTCTCTGCTCAGCGCCTTGAGCCTCAATGAAGAGTCTCTAGGTAAC
AGGAGAATTCGAGTGGATGTTGCTGATCAAGCACAGGATAAAGACAGGGATGATCGTTCTTTTGGCCGAGATAGAAATCG
GGACTCTGACAAAACAGATACAGACTGGAGGGCCCGTCCAACCACAGACAGCTTTGATGACTACCCGCCTAGAAGAGGTG
ATGATAGCTTTGGAGACAAGTACCGTGATCGTTACGATTCAGACCGGTATCGTGACGGCTATCGTGATGGCTATCGTGAC
GGTCCTCGCCGGAATATGGATCGCTATGGGGGCCGGGATCGATATGATGATCGGGGCAGCAGAGACTATGATAGGGGCTA
TGACTCCAGGATAGGCAGTGGCAGAAGAGCGTTTGGTAGTGGGTACCGAAGGGATGATGACTACAGAGGAGGTGGGGACC
GCTATGAAGACCAATACGACAGAAGGGACGATCGGTCGTGGGGGGTCCAGAGATGATTACTCTCCGGATGATTACAGGCG
TGATGATAGAGGTCCCCCGCAAAGACCCAAACTGAATCTAAAGCCTCAGAGTGCTCCTAAGGAAGATGATTCCTCTGCTA
GCACCTCCCAGTCCAGTCGAGCGGCATCCATCTTTGGAGGGGCAAAGCCTGTTGACACAGCCGCTAGAGAACGAGAAGTA
GAAGAACGGCTACAGAAGGAACAGGAGAAATTACAGCGTCAGCTGGATGAGCCAAAACTAGAACGACGGCCTCGGGAGAG
ACACCCAAGCTGGCGTAGTGAAGAAACTCAGGAGCGGGGAACGGTCAAGGACGGGAAGTGAGTCATCGCAGACTGGGACC
TCAGCCACATCTGGCAGAAATGCACGAAGGAGAGAGAGTGAAAAGTCTCTGGAAAATGAAATATTCAGTAAGGAGGAAGA
TTGTCAGTCTCCAACTTCTAAGCCTCCCAAACCTGATCAACCTCTAAAGGTAATGCCAGCCCCTCCACCAAAGGAGAATG
CTTGGTGAAGCGAAGCTCTAATCCTCCTGCTCAATCTCGGAGCTCAGACACAGAGCAGCAATCCCCTACAAGTGTTGGGG
GGAAAGTAGCTGCAGCTCAACCATCTGAAGAAGAACCATCAAGGAAAGATGAAAATAAAGTAGATGGGTTAAGTGTCCCA
AAAGGCCAAAGTGGGAACTCCAGCCGTGGTCCAGGAGATAGAGGGAACAGAGACCACTGGAAGGAGTCTGATAGGAAAGA
TGGCAAAAAGGATCAAGACTCTAGATCTGCACCTGAGCCAAAGAAACCTGAAGAAAATCCAGCCTCTAAATTCAGTTCTG
CAAGCAAGTATGCTGCTCTCTCAGTTGATGGTGAAGATGAAAATGAGGGAGAATATTATGCCGAA

Alignment

ORF - retro_lafr_294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.42 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TAKKKNKKGKTISLTDFLAEDGGTGGGSTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSIL
          .AKKKNKKGKTISLTDFLAEDGGTGGGSTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPID.SIL
Retrocopy SAKKKNKKGKTISLTDFLAEDGGTGGGSTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDHSIL

Parental  PTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEDSIKEFFRGLNISAVRLPREPSNPERLKGFGYAE
          PTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEDSIKEFFRGLNISAVRLPREPSNPERLKGFGYAE
Retrocopy PTAPRAAREPNIDRSRLPKSPPYTAFLGNLPYDVTEDSIKEFFRGLNISAVRLPREPSNPERLKGFGYAE

Parental  FEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPTTDSFDDYPP
          FEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPTTDSFDDYPP
Retrocopy FEDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPTTDSFDDYPP

Parental  RRGDDSFGDKYRDRYDSDRYRDGYRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGS
          RRGDDSFGDKYRDRYDSDR............PRR.MDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGS
Retrocopy RRGDDSFGDKYRDRYDSDRXXXXXXXXXXXXPRRNMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFGS

Parental  GYRRDDDYRGGGDRYEDRYDRRDDRSW-GSRDDYSRDDYRRDDRGPPQRPKLNLKPRSAPKEDDSSASTS
          GYRRDDDYRGGGDRYED.YDRRDDRSW.GSRDDYS.DDYRRDDRGPPQRPKLNLKP.SAPKEDDSSASTS
Retrocopy GYRRDDDYRGGGDRYEDQYDRRDDRSW>GSRDDYSPDDYRRDDRGPPQRPKLNLKPQSAPKEDDSSASTS

Parental  QSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQER-ERSRTG
          QSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQER.ERSRTG
Retrocopy QSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQER>ERSRTG

Parental  SESSQTGTSATSGRNARRRESEKSLENEIFSKEEDCHSPTSKPPKPDQPLKVMPAPPPKENAW-VKRSSN
          SESSQTGTSATSGRNARRRESEKSLENEIFSKEEDC.SPTSKPPKPDQPLKVMPAPPPKENAW.VKRSSN
Retrocopy SESSQTGTSATSGRNARRRESEKSLENEIFSKEEDCQSPTSKPPKPDQPLKVMPAPPPKENAW<VKRSSN

Parental  PPARSQSSDTEQQSPTSVGGKVAAAQPSEEGPSRKADENKVDGLSVPKGQSGNSSRGPGDGGNRDHWKES
          PPA.S.SSDTEQQSPTSVGGKVAAAQPSEE.PSRK.DENKVDGLSVPKGQSGNSSRGPGD.GNRDHWKES
Retrocopy PPAQSRSSDTEQQSPTSVGGKVAAAQPSEEEPSRK-DENKVDGLSVPKGQSGNSSRGPGDRGNRDHWKES

Parental  DRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEDYAE
          DRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGE.YAE
Retrocopy DRKDGKKDQDSRSAPEPKKPEENPASKFSSASKYAALSVDGEDENEGEYYAE

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_294 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 17 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278, retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294 ,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,