RetrogeneDB ID: retro_lafr_4

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:16856214..16857297(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000030960
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SEPT2
• Ensembl ID: ENSLAFG00000011964
• Aliases: None
• Description: None

Sequence

>retro_lafr_4
ATGTCTAAGCAGCCAGCTCAGTTCATAAATCCAGAAACACCTGGCTATGTTGGATTTGCCAATCTTCCTAATCAAGTTCA
CCGAAAATCAGTGAAAAAAGGTTTCGAGTTCACACTGATGGTTGTTGGTGAATCTGGACTGGGAAAGTCGACACTCATAA
ACAGCCTGTTCCTGACCGACCTCTACCCAGAAAGAGTCATACCTGGAGCTGCAGAAAAAATTGAGAGAACTGTCCAAATC
GAGGCCTCCACCGTGGAGATTGAAGAGCGAGGGGTCAAGCTGCGACTGACAGTAGTGGACACATCTGGCTACGGCGATGC
CATCAACTGCCGAGACTGTTTTAAGACCATCATCTCCTACATCGACGAGCAGTTTGAACGGTACCTGCACGATGAGAGCG
GCTTGAACAGGCGGCATATCATCGACAACAGGGTTCACTGCTGCTTCTACTTCATCTCCCCTTTCGGACACGGACTGAAG
CCCTTGGATGTTGCATTCATGAAGGCGATTCACAATAAGGTGAACATCGTGCCTGTCATCGCCAAGGCTGACACCCTCAC
GCTGAAGGAATGGGAGCGCTTAAAGAAAAGGATTCTGGATGAAATTGAAGAACATAGCATCAAAATCTATCACTTACCTG
ACGCAGAGTCAGATGAAGATGAAGATTTTAAAGAGCAGACCAGGCTTCTCAAGGCCAGCATCCCATTTTCGGTGGTCGGA
TCCAACCAGCTGACTGAAGCCAAAGGCAAGAAGGTCCGAGGCCGCCTCTACCCGTGGGGGGTGGTGGAGGTGGAGAACCC
AGAGCACAACGACTTCCTGAAGCTGAGGACCATGCTCGTAACTCATATGCAGGACCTCCAGGAGGTGACCCAGGACCTCC
ACTACGAGAACTTCCGCTCTGAGAGGCTCAAGAGAGGCGGCAGAAAAGTAGAGAATGAGGACATGAACAAAGACCAGATC
TTGCTGGAAAAGGAAGCTGAACTTCGCCACATGCAGGAGATGATCGCAAGGATGCAAGCTCAGATGCAAATACAGATGCA
GGCGGGGGACGGCGACGGCGGTGTGCACGGGCAGCACGTGTGA

Alignment

ORF - retro_lafr_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.77 %
• Parental protein coverage: 99.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQPAQFINPETPGYVGFANLPNQVHRKSVKKGFEFTLMVVGESGLGKSTLINSLFLTDLYPERVIPGAAE
          .QPAQFINPETPGYVGFANLPNQVHRKSVKKGFEFTLMVVGESGLGKSTLINSLFLTDLYPERVIPGAAE
Retrocopy KQPAQFINPETPGYVGFANLPNQVHRKSVKKGFEFTLMVVGESGLGKSTLINSLFLTDLYPERVIPGAAE

Parental  KIERTVQIEASTVEIEERGVKLRLTVVDTPGYGDAINCRDCFKTIISYIDEQFERYLHDESGLNRRHIID
          KIERTVQIEASTVEIEERGVKLRLTVVDT.GYGDAINCRDCFKTIISYIDEQFERYLHDESGLNRRHIID
Retrocopy KIERTVQIEASTVEIEERGVKLRLTVVDTSGYGDAINCRDCFKTIISYIDEQFERYLHDESGLNRRHIID

Parental  NRVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPVIAKADTLTLKERERLKKRILDEIEEHSIKIYHL
          NRVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPVIAKADTLTLKE.ERLKKRILDEIEEHSIKIYHL
Retrocopy NRVHCCFYFISPFGHGLKPLDVAFMKAIHNKVNIVPVIAKADTLTLKEWERLKKRILDEIEEHSIKIYHL

Parental  PDAESDEDEDFKEQTRLLKASIPFSVVGSNQLIEAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTMLITH
          PDAESDEDEDFKEQTRLLKASIPFSVVGSNQL.EAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTML.TH
Retrocopy PDAESDEDEDFKEQTRLLKASIPFSVVGSNQLTEAKGKKVRGRLYPWGVVEVENPEHNDFLKLRTMLVTH

Parental  MQDLQEVTQDLHYENFRSERLKRGGRKVENEDMNKDQILLEKEAELRRMQEMIARMQAQMQMQMQAGDGD
          MQDLQEVTQDLHYENFRSERLKRGGRKVENEDMNKDQILLEKEAELR.MQEMIARMQAQMQ.QMQAGDGD
Retrocopy MQDLQEVTQDLHYENFRSERLKRGGRKVENEDMNKDQILLEKEAELRHMQEMIARMQAQMQIQMQAGDGD

Parental  GGVHGHHV
          GGVHG.HV
Retrocopy GGVHGQHV

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_4 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002608	1 retrocopy	retro_btau_1185,
Canis familiaris	ENSCAFG00000012960	1 retrocopy	retro_cfam_1477,
Choloepus hoffmanni	ENSCHOG00000008715	5 retrocopies	retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Callithrix jacchus	ENSCJAG00000006122	1 retrocopy	retro_cjac_1501,
Cavia porcellus	ENSCPOG00000013687	1 retrocopy	retro_cpor_845,
Loxodonta africana	ENSLAFG00000011964	1 retrocopy	retro_lafr_4 ,
Macropus eugenii	ENSMEUG00000016519	1 retrocopy	retro_meug_39,
Myotis lucifugus	ENSMLUG00000007108	1 retrocopy	retro_mluc_1594,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Mustela putorius furo	ENSMPUG00000000166	1 retrocopy	retro_mputfur_436,
Nomascus leucogenys	ENSNLEG00000013873	1 retrocopy	retro_nleu_1848,
Otolemur garnettii	ENSOGAG00000004457	1 retrocopy	retro_ogar_2239,
Pteropus vampyrus	ENSPVAG00000000558	1 retrocopy	retro_pvam_448,
Rattus norvegicus	ENSRNOG00000017952	1 retrocopy	retro_rnor_1110,
Ictidomys tridecemlineatus	ENSSTOG00000013357	1 retrocopy	retro_itri_1227,
Drosophila melanogaster	FBgn0011710	1 retrocopy	retro_dmel_35,