RetrogeneDB ID: retro_cfam_338

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 10:773126..773815(+)
• Located in intron of: ENSCAFG00000000134

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7
• Ensembl ID: ENSCAFG00000008021
• Aliases: None
• Description: Canis lupus familiaris ribosomal protein L7 (RPL7), mRNA. [Source:RefSeq mRNA;Acc:NM_001252227]

Sequence

>retro_cfam_338
GAAAAAGCTATAAGGAATTCCATAGAGTTGAAGATCAAGCATCTGAGAAAAAAGTTTGCCCCAACGATGCTTTGAAAGGC
AAGGAGGAAGCTTATTTATGAAAAAGATAGGCATTACCACAAGGAATACAGGCAGATATACAGAACTGAGATTTGAATGG
CGAGGATGGCAAGGAAAGCTGGCAACTTCTATGTGTCTGCAGAACCCAAATTGGCATTTGTCATCAGCATCAGAGGTATC
AGTGGTGTGAGCCCAAAGATTCGAAAGGTGTTGCAGCTTCTTTGCCTTCGCCAGATCTTCAATGGCACCTTTGTTAAGCT
TAACAAGGCTTCAGTTAACATGCTAAGGATTGTGGAACCATATATAGCATGGGAGTACCCAAACCTGAAGTCAGTGAATG
AATTGATCTACAAGCGTTGTTATGGCAAGATCAACAAGAAGCGAATTGCCCTGACAGATAACACACTGATTGCCCCATCT
CTTGGTAAATATGGCATCATCTGCATGAAGGATCTGATTCACGAGATCTGTACTGTTGGAAAATGTTTCAAAGAAGCAAA
CAATTTTTTATGACCCTGCAAATTATCTTCTGCATACAGGGGAATGAAGAAAAAAGCACCCATTTTGTAGAAGGTGGAGA
TGCTAGCAACAGGGTAGACCAGATCAATAGGCTTATTAGAAGGATGAAC

Alignment

ORF - retro_cfam_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 92.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMARKAGNFYVPAEPK
          .K..RN..ELKIK.LRKKFA..ML.KARRKLIYEK..HYHKEYRQ.YRTEI.MARMARKAGNFYV.AEPK
Retrocopy EKAIRNSIELKIKHLRKKFAPTML*KARRKLIYEKDRHYHKEYRQIYRTEI*MARMARKAGNFYVSAEPK

Parental  LAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASVNMLRIVEPYIAWGYPNLKSVNELIYKRG
          LAFVI.IRGI.GVSPK.RKVLQLL.LRQIFNGTFVKLNKASVNMLRIVEPYIAW.YPNLKSVNELIYKR.
Retrocopy LAFVISIRGISGVSPKIRKVLQLLCLRQIFNGTFVKLNKASVNMLRIVEPYIAWEYPNLKSVNELIYKRC

Parental  YGKINKKRIALTDNTLIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKK-KTTHF
          YGKINKKRIALTDNTLIA.SLGKYGIICM.DLIHEI.TVGK.FKEANNFL.P.KLSS...GMKK.K.THF
Retrocopy YGKINKKRIALTDNTLIAPSLGKYGIICMKDLIHEICTVGKCFKEANNFL*PCKLSSAYRGMKK<KSTHF

Parental  VEGGDAGNREDQINRLIRRMN
          VEGGDA.NR.DQINRLIRRMN
Retrocopy VEGGDASNRVDQINRLIRRMN

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	454.47 RPM
SRP017611_brain	0.00 RPM	183.00 RPM
SRP017611_kidney	0.07 RPM	893.22 RPM
SRP017611_liver	0.07 RPM	289.69 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_338 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_338 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_338 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 75 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001821	5 retrocopies	retro_amel_1230, retro_amel_1632, retro_amel_760, retro_amel_933, retro_amel_937,
Canis familiaris	ENSCAFG00000001728	4 retrocopies	retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Canis familiaris	ENSCAFG00000008021	28 retrocopies	retro_cfam_1039, retro_cfam_1075, retro_cfam_1079, retro_cfam_1167, retro_cfam_1209, retro_cfam_1236, retro_cfam_1270, retro_cfam_1308, retro_cfam_1390, retro_cfam_1436, retro_cfam_1445, retro_cfam_1453, retro_cfam_1524, retro_cfam_1541, retro_cfam_1699, retro_cfam_1755, retro_cfam_1855, retro_cfam_1856, retro_cfam_2051, retro_cfam_2192, retro_cfam_338 , retro_cfam_403, retro_cfam_563, retro_cfam_609, retro_cfam_737, retro_cfam_74, retro_cfam_922, retro_cfam_998,
Dasypus novemcinctus	ENSDNOG00000017654	15 retrocopies	retro_dnov_1561, retro_dnov_1692, retro_dnov_182, retro_dnov_1893, retro_dnov_209, retro_dnov_2158, retro_dnov_2568, retro_dnov_264, retro_dnov_2657, retro_dnov_279, retro_dnov_287, retro_dnov_365, retro_dnov_655, retro_dnov_77, retro_dnov_971,
Felis catus	ENSFCAG00000028446	6 retrocopies	retro_fcat_1643, retro_fcat_230, retro_fcat_255, retro_fcat_338, retro_fcat_342, retro_fcat_945,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,