RetrogeneDB ID: retro_cfam_1478

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:28014179..28015334(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000012222
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:E2QW85]

Sequence

>retro_cfam_1478
ATGGGAAAGGAAAAGACTCATATCAACATCGTCATCATTGGACACATAGATTGGGGCAAGTCTACCACTACTGGCCATCT
GATCTACAAATGTGGTGGGATCGACAAAAGAACCATAGAAAAATTTGAGAAGGAGGCTGCTGAGATGGAAAAAGGCTCCT
TCAAGTCAGCCTCGGTCTTGGATAAACTGAAAGCTGAATGTGAACATGGTATCACCATTGATATCACCCTGTGGCAATTC
AAGACCAGCAAGTATTACGTGACCATCATTGATACCCCAGGACACAGAGACTTTATCAAAAACATGATTACAGACACATC
TCAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCAGGTATCTCCAAGAATGAGCAGACCC
ACGAGCATGCCCTTCTGGCTTACACACTGAGTGTAAAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCA
CCCTGCAGCCAGAAGAGATATGAGGAAATCGTTAAGGAAGTCAGCACCTACATTAAGAAAATTGGCTACAACCCCAACAC
AGTAGCATTTGTGCCAATTTCTGGTTAGAATGGTGACAACATGCTGGAGCCAAGTGCTAACATGCCTTGGTTCAAGGGAT
GGAAAGTCCCCCATAAAGATGTGAAAGCCAGTGGAACCACACTGCTTGGAGCTCTGGATTCCATTCTGCTGCCAACTCGT
CCAACTGATAAGCCCTTGCATCTGCCTCTCCAGGGTGTCTACAAAATTGGTGGTATTGGTACTGTCCCAGTGGGGCGAGT
GGAGATTGGTGTACTTAAGCCTGGCATGGTGGTCACCCCTTCTCTGGTCAATGTTACAACTGAAGTAAAGTCTGTTGAAA
TGTACCATGAAGCTTTGAGTGAGGCTCTTCCTGGGGACAATGTGGGTTTCAATGTCAAGAATGTATCTGTCAAAGATGTT
CATCGTGGCAACGTGGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGGCTTCGTGGCTCAGGTGATTTTCCT
GAACCGTCCAGGCCAAATCAGTGCTGGATATACACCTGTGCTGGATTGTCACACAGCTCACATTGCTTGCAAGTTTGCTG
AGCTGAAGGAGAAGATAGATCGTCTTTCTGGAAGA

Alignment

ORF - retro_cfam_1478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.87 %
• Parental protein coverage: 83.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
          MGKEKTHINIV.IGH.D.GKSTTTGHLIYKCGGIDKRTIEKFEKEAAEM.KGSFK.A.VLDKLKAE.E.G
Retrocopy MGKEKTHINIVIIGHIDWGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMEKGSFKSASVLDKLKAECEHG

Parental  ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
          ITIDI.LW.F.TSKYYVTIID.PGHRDFIKNMIT.TSQADCAVLIVAAGVGEFEAGISKN.QT.EHALLA
Retrocopy ITIDITLWQFKTSKYYVTIIDTPGHRDFIKNMITDTSQADCAVLIVAAGVGEFEAGISKNEQTHEHALLA

Parental  YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPNTVAFVPISGWNGDNMLEPSANMPW
          YTL.VKQLIVGVNKMDSTEPP.SQKRYEEIVKEVSTYIKKIGYNPNTVAFVPISG.NGDNMLEPSANMPW
Retrocopy YTLSVKQLIVGVNKMDSTEPPCSQKRYEEIVKEVSTYIKKIGYNPNTVAFVPISG*NGDNMLEPSANMPW

Parental  F-GWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF
          F.GWKV..KD..ASGTTLL.ALD.IL.PTRPTDKPL.LPLQ.VYKIGGIGTVPVGRVE.GVLKPGMVVT.
Retrocopy FKGWKVPHKDVKASGTTLLGALDSILLPTRPTDKPLHLPLQGVYKIGGIGTVPVGRVEIGVLKPGMVVTP

Parental  APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVHRGNVAGDSKNDPPMEAAGFTAQVIILNHP
          ..VNVTTEVKSVEM.HEALSEALPGDNVGFNVKNVSVKDVHRGNVAGDSKNDPPMEAAGF.AQVI.LN.P
Retrocopy SLVNVTTEVKSVEMYHEALSEALPGDNVGFNVKNVSVKDVHRGNVAGDSKNDPPMEAAGFVAQVIFLNRP

Parental  GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGK
          GQISAGY.PVLDCHTAHIACKFAELKEKIDR.SG.
Retrocopy GQISAGYTPVLDCHTAHIACKFAELKEKIDRLSGR

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
SRP012049_cerebellum	0.04 RPM	0.50 RPM
SRP017611_brain	0.08 RPM	0.32 RPM
SRP017611_kidney	1.32 RPM	3.63 RPM
SRP017611_liver	0.15 RPM	0.94 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1478 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1478 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012222	1 retrocopy	retro_cfam_1478 ,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
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,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,