RetrogeneDB ID: retro_ocun_720

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:121743059..121743863(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSOCUG00000005867
• Aliases: None
• Description: actin, gamma 1 [Source:HGNC Symbol;Acc:144]

Sequence

>retro_ocun_720
CCCTGAGCCATCTTCCCCTCTCCTGAAAGGCACCCCCATCACCAAGGTGTGATGAGGGGCATGGGCTAGAAGGACTCCTA
CATAGGCAATAAAACCCAGAGCAAGAGAGGCATCATGACCCTGAAGTACCCTATGCAGCACAGCATTGTCAACAACTGGG
CCAACGTGGAGAAGATCTGGCACCAAACCTTCTACAACGAGCTGTGTGTGGCCCCTGAGAAGCACTCCAGGCTGCTGCCT
GAGAAGCCCCTGAACACCAACAGAGAGAAGATCATGTCTGAGACCTTCAAAACCACAGCCATGTCTGTGGCCATCCAGAC
GGTGCTGTCCCCATACGCCTCTCACTGCACGAGCGACATTGTGATGAACTCCGGCAATAGGTCACCCACATAGTGCACAT
CCTTGAAGGGGTATGCCCTTCCCCAGTCATCCTGCATCCAGATGTGACTGACAGGGACCTGACTGACAACCTTAGAAACA
TCCTCAGGGAGAGTGGCTTCACTGTCACCATTATGGCAGTGTTGGAAATGGTGCACAACTTAAAGGAGTTCTGCTACTTG
ACCTGGACTTCAAGCAGGAGATAGTAACCATGGCATCCTCCTGCTCCCTGGAGAAGAACTATAAACTGCCCAATGACAAA
GTGATCCCCACTGGCACTGGTGGTTCTGCTGTCTCCAGGTGCTCTTCCAGCCTTCCTTCCTGGGCATGGAGTCATGTGGC
ATCCATAAAACTACCTTCAACTCCATCATGAAGTGTGACGTCAACATGAAAGGACCTATACACCAATACTGTGCTGTCCA
GGGG

Alignment

ORF - retro_ocun_720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.4 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PRAVFPSLVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRV
          P.A.FPS....P.HQGVM.GMG.KDSY.G...QSKRGI.TLKYP..H.IV.NW...EKIWH.TFYNEL.V
Retrocopy P*AIFPSPERHPHHQGVMRGMG*KDSYIGNKTQSKRGIMTLKYPMQHSIVNNWANVEKIWHQTFYNELCV

Parental  APEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDG-VTHTVPI
          APE.H..LL.E.PLN...NREK...IM...........AIQ.VLS.YAS..T..IVM.SG...VTH.V.I
Retrocopy APEKHSRLLPEKPLN--TNREK---IMXXXXXXXXXXXAIQTVLSPYASHCTSDIVMNSGNR<VTHIVHI

Parental  YEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVA-LDFEQEMATAASSS
          .EG......IL..D...RDLTD.L..IL.E.G...T..A..E.V...KE..CY...LDF.QE..T.ASS.
Retrocopy LEGVCPSPVILHPDVTDRDLTDNLRNILRESGFTVTIMAVLEMVHNLKE-FCYLT<LDFKQEIVTMASSC

Parental  SLEKSYELPDGQVITIGNER-FRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSG
          SLEK.Y.LP...VI..G....F.C...LFQPSFLGMESCGIH.TTFNSIMKCDV.............G
Retrocopy SLEKNYKLPNDKVIPTGTGG<FCCLQVLFQPSFLGMESCGIHKTTFNSIMKCDVNMKGPIHQYCAVQG

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
SRP017611_brain	0.00 RPM	1055.70 RPM
SRP017611_kidney	0.00 RPM	804.57 RPM
SRP017611_liver	0.00 RPM	475.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_720 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_720 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macropus eugenii	ENSMEUG00000016247	57 retrocopies	retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Nomascus leucogenys	ENSNLEG00000013385	15 retrocopies	retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus	ENSOCUG00000004074	1 retrocopy	retro_ocun_38,
Oryctolagus cuniculus	ENSOCUG00000005867	1 retrocopy	retro_ocun_720 ,
Oryctolagus cuniculus	ENSOCUG00000008193	3 retrocopies	retro_ocun_1306, retro_ocun_1421, retro_ocun_919,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,