RetrogeneDB ID: retro_rnor_684

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:44912121..44912598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cfl2
• Ensembl ID: ENSRNOG00000045892
• Aliases: None
• Description: cofilin-2 [Source:RefSeq peptide;Acc:NP_001102452]

Sequence

>retro_rnor_684
GCATCTGGAGTTACAGTGAATGATGAAGTCATCAAAGTTCTTAATGATATGAAAGTAAAATCTTCTACATAGGAGGAGAT
TGAAAAAGAAAGAAAGCAGTTCTCTTCTGTCTAAGCAATGACAAAAGACGAGAAAGCAAAGCAGATCTTGGTGGGTGACA
TCGGTGATACTGTAGAGGACCCCTACACATCTTTTGTGAAATTGCTACCTCTGAATGGTTGCCGATATGCTTTGTACGAT
GCCACATACGAAACAAAAGAATCTAAGAAAGAAGACCTAGTGTTTATATTCTGGGCTCCTAAAAGTGCACGGTTAAAAAG
CAAGATGATTTATGCTAACTCTAAAAATGCCATTAAAAAATTTATAGGTATTAAACATAAGTGGCAAGTAAATGGCTTGG
ACGATATTAAGGACTGCATGACACTGGGAGAGAAACTGGGAGGCAGTGTTGTAGTTTCCCTGGAAGGAAAGCCACTG

Alignment

ORF - retro_rnor_684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.43 %
• Parental protein coverage: 99.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASGVTVNDEVIKVFNDMKVRKSSTQEEIK-KRKKAVLFCLSDDKRQIIVEEAKQILVG-DIGDTVEDPYT
          ASGVTVNDEVIKV.NDMKV.KSST.EEI..KRKKAVLFCLS.DKR.....E.K..L.G.DIGDTVEDPYT
Retrocopy ASGVTVNDEVIKVLNDMKV-KSST*EEIE<KRKKAVLFCLSNDKRR----ESKADLGG>DIGDTVEDPYT

Parental  SFVKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQVNG
          SFVKLLPLN.CRYALYDATYETKESKKEDLVFIFWAP.SA.LKSKMIYA.SK.AI.KKF.GIKH.WQVNG
Retrocopy SFVKLLPLNGCRYALYDATYETKESKKEDLVFIFWAPKSARLKSKMIYANSKNAI-KKFIGIKHKWQVNG

Parental  LDDIKDRSTLGEKLGGSVVVSLEGKPL
          LDDIKD..TLGEKLGGSVVVSLEGKPL
Retrocopy LDDIKDCMTLGEKLGGSVVVSLEGKPL

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	52.27 RPM
SRP017611_kidney	0.00 RPM	60.92 RPM
SRP017611_liver	0.00 RPM	30.53 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_684 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_684 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015508	1 retrocopy	retro_amel_1347,
Canis familiaris	ENSCAFG00000032562	1 retrocopy	retro_cfam_1006,
Cavia porcellus	ENSCPOG00000008996	1 retrocopy	retro_cpor_1003,
Echinops telfairi	ENSETEG00000006010	3 retrocopies	retro_etel_1579, retro_etel_1622, retro_etel_684,
Felis catus	ENSFCAG00000008480	2 retrocopies	retro_fcat_1223, retro_fcat_1395,
Latimeria chalumnae	ENSLACG00000018011	1 retrocopy	retro_lcha_23,
Loxodonta africana	ENSLAFG00000010579	1 retrocopy	retro_lafr_1041,
Macropus eugenii	ENSMEUG00000000739	11 retrocopies	retro_meug_1026, retro_meug_1138, retro_meug_125, retro_meug_1266, retro_meug_1666, retro_meug_1791, retro_meug_2025, retro_meug_2062, retro_meug_210, retro_meug_321, retro_meug_668,
Microcebus murinus	ENSMICG00000009237	1 retrocopy	retro_mmur_493,
Monodelphis domestica	ENSMODG00000012949	1 retrocopy	retro_mdom_171,
Mus musculus	ENSMUSG00000062929	1 retrocopy	retro_mmus_660,
Otolemur garnettii	ENSOGAG00000032321	1 retrocopy	retro_ogar_2346,
Pteropus vampyrus	ENSPVAG00000002798	1 retrocopy	retro_pvam_398,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Rattus norvegicus	ENSRNOG00000020660	2 retrocopies	retro_rnor_1354, retro_rnor_693,
Rattus norvegicus	ENSRNOG00000045892	1 retrocopy	retro_rnor_684 ,
Sarcophilus harrisii	ENSSHAG00000004732	1 retrocopy	retro_shar_528,
Sus scrofa	ENSSSCG00000001959	2 retrocopies	retro_sscr_1198, retro_sscr_327,
Ictidomys tridecemlineatus	ENSSTOG00000001675	3 retrocopies	retro_itri_1313, retro_itri_581, retro_itri_632,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,
Vicugna pacos	ENSVPAG00000003273	1 retrocopy	retro_vpac_644,