RetrogeneDB ID: retro_ecab_93

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 18:34530152..34531541(-)
• Located in intron of: ENSECAG00000011111

Retrocopy information

• Ensembl ID: ENSECAG00000001048
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: eca-mir-703
• Ensembl ID: ENSECAG00000020363
• Aliases: EEF1A1, EF-1A, EF-Tu, EF1A, eEF1A-1
• Description: eca-mir-703 [Source:miRBase;Acc:MI0012753]

Sequence

>retro_ecab_93
ATGGGGAAGGAAAAGACTCATATCAACATTGTCGTCATTGGACACGTCGATTCGGGCAAGTCCACCACGACTGGCCACCT
GATCTACAAGTGCGGTGGGATCGACAAAAGAACCATTGAGAAATTCGAGAAGGAGGCTGCTGAGATGGGAAAGGGCTCCT
TCAAGTACGCCTGGGTCTTGGATAAACTGAAAGCTGAACGTGAGCGTTGTATCACCATTGATATCTCCCTGTGGAAATTC
GAGACCAGCAAGTATTATGTGACCATCATTGATGCCCCCGGACAGAGAGACTTCATCAAAAACATGATTACAGGCACGTC
TCAGGCTGACTGTGCTGTCCTGATTGTCGCTGCTGGTGTTGGTGAATTTGAAGCAGGTATCTCCAAGAATGGGCAGACCC
GTGAGCATGCCCTTCTGGCTTACACACTGGGTGTGAAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCA
CCCTACAGCCAGAAGAGATATGAGGAAATCGTTAAGGAAGTCAGCACCTACATTAAGAAAATTGGCTACAACCCAGACAC
AGTTGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCAAGTGCTAATATGCCTTGGTTCAAGGGAT
GGAAAGTCACCCGTAAAGATGGCAATGCCAGTGGAACTACGCTGCTTGAAGCTCTGGATTGCATCCTGCCACCAACTCGT
CCAACTGATAAGCCCTTGCGTCTGCCCCTCCAGGACGTCTACAAAATTGATGGTATCGGTACTGTCCCTGTGGGCCGAGT
GGAGACTGGTGTTTTGAAACCTGGCATGGTGGTCACCTTTGCTCCAGTCAATGGTACAACTGAAGTAAAGTCTGTTGAAA
TGCATCATGAAGCTTTGAGCAAAGCTCTTCCTGGGGACAACGTGGGCTTCAACGTCAAGAACGTGTCCGTCAAAGATGTT
CGCCGTGGCAATGTGGCTGGTGACAGCAAAAATGATCCACCAATGGAAGCAGCTGGCTTCACAGCTCAGGTGATTATCCT
GAACCATCCAGGCCAAATCAGTGCTGGGTATGCACCTGTGCTGGATTGTCACACAGCTCACATTGCTTGCAAGTTTGCTG
AGCTGAAGGAGAAGATTGATCGTCGTTCTGGAAAGAAGCTGGAAGATGGCCCCAAATTCTTGAAATCTGGTGATGCTGCC
ATCGTTGATATGGTTCCTGGCAAGCCCATGTGTGTTGAGAGCTTTTCTGACTATCCTCCTCTGGGCCGTTTTGCTGTTCG
TGACATGAGACAGATGGTTGCTGTGGGTGTCATCAAAGCAGTGGACAAGAAAGCAGCTGGAGCTGGCAAGGTCACCAAGT
CTGCCCAGAAGGCTCAGAAGGCTAAATGA

Alignment

ORF - retro_ecab_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
          MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERER.
Retrocopy MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERC

Parental  ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
          ITIDISLWKFETSKYYVTIIDAPG.RDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
Retrocopy ITIDISLWKFETSKYYVTIIDAPGQRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA

Parental  YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW
          YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW
Retrocopy YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW

Parental  FKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF
          FKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKI.GIGTVPVGRVETGVLKPGMVVTF
Retrocopy FKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIDGIGTVPVGRVETGVLKPGMVVTF

Parental  APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP
          APVN.TTEVKSVEMHHEALS.ALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP
Retrocopy APVNGTTEVKSVEMHHEALSKALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP

Parental  GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPP
          GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPP
Retrocopy GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPP

Parental  LGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          LGRFAVRDMRQ.VAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
Retrocopy LGRFAVRDMRQMVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK

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
SRP021940_articular_cartilage	1.36 RPM	831.49 RPM
SRP021940_cerebellum	0.52 RPM	347.32 RPM
SRP021940_embryo	1.48 RPM	697.24 RPM
SRP021940_placental_villous	0.91 RPM	528.74 RPM
SRP021940_synovial_membrane	1.24 RPM	599.36 RPM
SRP021940_testis	0.58 RPM	249.83 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_93 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_93 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_93 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 149 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014534	3 retrocopies	retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000020363	2 retrocopies	retro_ecab_66, retro_ecab_93 ,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Felis catus	ENSFCAG00000030977	14 retrocopies	retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683, retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Homo sapiens	ENSG00000156508	27 retrocopies	retro_hsap_1093, retro_hsap_1181, retro_hsap_1567, retro_hsap_1671, retro_hsap_190, retro_hsap_2302, retro_hsap_2455, retro_hsap_2637, retro_hsap_2712, retro_hsap_278, retro_hsap_283, retro_hsap_2896, retro_hsap_2920, retro_hsap_2967, retro_hsap_2983, retro_hsap_3239, retro_hsap_3291, retro_hsap_3314, retro_hsap_363, retro_hsap_3701, retro_hsap_3706, retro_hsap_3758, retro_hsap_3825, retro_hsap_3917, retro_hsap_4220, retro_hsap_4730, retro_hsap_989,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Myotis lucifugus	ENSMLUG00000013537	24 retrocopies	retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furo	ENSMPUG00000003816	6 retrocopies	retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furo	ENSMPUG00000004271	10 retrocopies	retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Oryctolagus cuniculus	ENSOCUG00000008481	3 retrocopies	retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Ochotona princeps	ENSOPRG00000016685	6 retrocopies	retro_opri_1049, retro_opri_1076, retro_opri_1197, retro_opri_298, retro_opri_325, retro_opri_383,
Sus scrofa	ENSSSCG00000004489	4 retrocopies	retro_sscr_169, retro_sscr_492, retro_sscr_612, retro_sscr_758,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Tursiops truncatus	ENSTTRG00000000114	19 retrocopies	retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,