RetrogeneDB ID: retro_lcha_39

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126738.1:1917645..1918777(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000017125
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: eef1a1b
• Ensembl ID: ENSLACG00000002952
• Aliases: None
• Description: eukaryotic translation elongation factor 1 alpha 1b [Source:ZFIN;Acc:ZDB-GENE-050417-327]

Sequence

>retro_lcha_39
ATGGGAAAGGAAAAGATCCACATCAACATTGTGGTCATTGACCACGTCGACTCTGGTAAATCCACCACCACTGGTCACCT
CATCTACAAATGCGGTGGAATTGACAAGAGAACCATTGAGAAATTTGAGAAGGAAGCTGCTGAGATGGGGAAGGGCTCCT
TCAAGTATGCCTGGGTTCTGGACAAACTGAAGGCAGAGCATGAGCGTACTGATATCGCCCTGTGGAAGTTTGAGACCACC
AAATACTACATCACCATTATTGATGCCCCTGGACACAGAGACTTCATCAAGAACATGATCACTGGAACCTCCCAGGCAGA
TTGTGCTGTGCTGATTGTTGCTGGCGGTGTTGGTGAGTTTGAAGCTGGTATCTCCAAGAATGGACAGACCCGTGAGCATG
CCCTTTTGGCCTACACCTTGGGTGTGAAACAGCTTGTTGTTGGAGTCAACAAGATGGATTCCACTGAGCCTCCCTACAGT
GAGAAACGTTACAATGAAATCACCAAGGAAGTGAGTGCCTACATCAAGAAGATTGGCTACAACCCTGCCTCTGTGGCCTT
TGTCCCCATCTCTGGCTGGCATGGTGACAACATGCTGGAGGCCAGCCCCAACATGCCCTGGTTCAAAGGGTGGAAGATTG
AGAGGAAGGAAAATAATGTTAGCGGAGTTACCCTACTGGAGGCTTTGGACTATCGTTCCTCCAACACGTCCTACTGACAA
ACCTCTCCGTCTGCTCCTGCAAGATGTCTACAAGATTGGAGGTATTGGTACCGTGCCAGTTGGCCGTGTTGAAACTGGAG
TCCTGAAGCCTGGTACAGTTGTGACTTTTGCTCCTGCCAACCTCACCACTGAAGTCAAGTCTGTGGAAATGCACCATGAA
GCCCTGCACGAGGCCCTTCCTGGCGATAACGTTGGCTTCAATGTGAAAAACGTCTCAGTCAAGGATATCTGTCGTGGAAA
CGTTGCTGGAGACAGCAAGAATGACCCTCCAGCTGAGGCTGGTAGCTTCACTGCTCAGGTCATCATCCTGAACCACCCTG
GTCAGATCAGTGCTGGCTATGCCCCAGTGCTGGACTGTCATACTGCTCACATTGCATGCAAGTTTGCTGAGCTGAAGGAG
AAGATTGACCGC

Alignment

ORF - retro_lcha_39 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.03 %
• Parental protein coverage: 82.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKERTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
          MGKE..HINIVVI.HVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAE.ER.
Retrocopy MGKEKIHINIVVIDHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAEHER-

Parental  ITIDIALWKFETGKYYITIIDAPGHRDFIKNMITGTSQADCGVLIVAAGVGEFEAGISKNGQTREHALLA
          ...DIALWKFET.KYYITIIDAPGHRDFIKNMITGTSQADC.VLIVA.GVGEFEAGISKNGQTREHALLA
Retrocopy --TDIALWKFETTKYYITIIDAPGHRDFIKNMITGTSQADCAVLIVAGGVGEFEAGISKNGQTREHALLA

Parental  YTLGVKQLIVGVNKMDSTEPPYNQERYQEIVKEVGTYIKKIGYNPDAVAFVPISGWNGDNMLEPSPNMTW
          YTLGVKQL.VGVNKMDSTEPPY...RY..............GYNP..VAFVPISGW.GDNMLE.SPNM.W
Retrocopy YTLGVKQLVVGVNKMDSTEPPYSEKRYXXXXXXXXXXXXXXGYNPASVAFVPISGWHGDNMLEASPNMPW

Parental  FKGWNIKNKNKNCVSGCTLLEALD-AIEPPSRPTDRPLRLPLQDVYKIGGIGTVPVGRVETGYLKPNMLV
          FKGW.I..K..N.VSG.TLLEALD....P..RPTD.PLRL.LQDVYKIGGIGTVPVGRVETG.LKP...V
Retrocopy FKGWKIERKENN-VSGVTLLEALD>IVPP-TRPTDKPLRLLLQDVYKIGGIGTVPVGRVETGVLKPGTVV

Parental  TFSPANITTEVKSVEMHHESLSQAQPGDNVGFNVKNVSVKDIRRGNVAGDSKNDPPQEAGSFIAQVIILN
          TF.PAN.TTEVKSVEMHHE.L..A.PGDNVGFNVKNVSVKDI.RGNVAGDSKNDPP.EAGSF.AQVIILN
Retrocopy TFAPANLTTEVKSVEMHHEALHEALPGDNVGFNVKNVSVKDICRGNVAGDSKNDPPAEAGSFTAQVIILN

Parental  HPGQISAGYTPVLDCHTAHISCKFAELLEKIDR
          HPGQISAGY.PVLDCHTAHI.CKFAEL.EKIDR
Retrocopy HPGQISAGYAPVLDCHTAHIACKFAELKEKIDR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
DRP000627_gill	384.44 RPM	266.12 RPM
DRP000627_kidney	325.91 RPM	213.12 RPM
DRP000627_pectoral_fin	686.27 RPM	586.42 RPM
DRP000627_pelvic_fin	938.34 RPM	854.38 RPM
DRP000627_pharynx	121.21 RPM	86.67 RPM
DRP000627_tail_muscle	91.69 RPM	74.59 RPM

ChIP-Seq

Latimeria chalumnae was not studied using ChIP-Seq data.

EST

Latimeria chalumnae was not studied using EST data.

TSS

Latimeria chalumnae was not studied using FANTOM5 data.

Lab

retro_lcha_39 was not experimentally validated.

Homology

Retrocopy orthology:

Latimeria chalumnae 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 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Latimeria chalumnae	ENSLACG00000002952	1 retrocopy	retro_lcha_39 ,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Macropus eugenii	ENSMEUG00000005018	23 retrocopies	retro_meug_1067, retro_meug_110, retro_meug_1160, retro_meug_1240, retro_meug_1334, retro_meug_135, retro_meug_1421, retro_meug_1451, retro_meug_1465, retro_meug_1501, retro_meug_1662, retro_meug_1690, retro_meug_1710, retro_meug_1829, retro_meug_2023, retro_meug_2044, retro_meug_2050, retro_meug_316, retro_meug_601, retro_meug_755, retro_meug_792, retro_meug_850, retro_meug_920,
Myotis lucifugus	ENSMLUG00000016760	1 retrocopy	retro_mluc_1250,
Mustela putorius furo	ENSMPUG00000008289	3 retrocopies	retro_mputfur_1030, retro_mputfur_609, retro_mputfur_761,
Nomascus leucogenys	ENSNLEG00000010060	2 retrocopies	retro_nleu_11, retro_nleu_1489,
Ornithorhynchus anatinus	ENSOANG00000004908	1 retrocopy	retro_oana_73,
Otolemur garnettii	ENSOGAG00000004630	8 retrocopies	retro_ogar_1067, retro_ogar_2034, retro_ogar_2329, retro_ogar_2497, retro_ogar_2583, retro_ogar_3191, retro_ogar_3270, retro_ogar_643,
Ictidomys tridecemlineatus	ENSSTOG00000028862	1 retrocopy	retro_itri_1028,
Tursiops truncatus	ENSTTRG00000001835	1 retrocopy	retro_ttru_993,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,