RetrogeneDB ID: retro_ocun_1397

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:6974850..6975340(+)
• Located in intron of: ENSOCUG00000017747

Retrocopy information

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

Parental gene information

• Parental gene symbol: CFL2
• Ensembl ID: ENSOCUG00000009383
• Aliases: None
• Description: cofilin 2 (muscle) [Source:HGNC Symbol;Acc:1875]

Sequence

>retro_ocun_1397
GCTTCTGGAGTTACAGTGAATGATGAAGTCATCAAAGTTTTTAATGATATGAAAGTAAAGAAATGTTCTACACAAGAGGA
GATCAAAAAAGAAAGAAAGCAGTTCTCTTCTGTTTAAGTGATGACAAAAGACAAATAATTGTAGAGGAAGCAAAGCAGAT
CTTGGTGGGTGACATTGGTGATACTGTAGAGGACCCCTACACATCTTCTGTGAAGTTGCTACCTCTGAATGATTCCGATA
TGCTTTGTACGATGCCACATATGAAACAGAAGAGTCTAAGAAAGAAGACCTAGTGTTTATATCCTGGGGTCCTGAAAGTG
CACCTTTGAAAAGCAGTATGATTTATGCTAGCTCTAAAGATGCCATTAAAAAGAAATTTACAGGGATTAAACACGAATGG
CAAGTGAGTGGCTTGGATGACATCAAGGACCGTTCAACACTTGGAGAGAAATTGGGAGGCAGTGCAGTAGTTTCACTTGA
AGGAAAACCA

Alignment

ORF - retro_ocun_1397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.34 %
• Parental protein coverage: 98.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASGVTVNDEVIKVFNDMKVRKSSTQEEIKK-RKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDPYTS
          ASGVTVNDEVIKVFNDMKV.K.STQEEIKK.RKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDPYTS
Retrocopy ASGVTVNDEVIKVFNDMKVKKCSTQEEIKK<RKKAVLFCLSDDKRQIIVEEAKQILVGDIGDTVEDPYTS

Parental  FVKLLPLNDC-RYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQVNG
          .VKLLPLND..RYALYDATYET.ESKKEDLVFI.W.PESAPLKS.MIYASSKDAIKKKFTGIKHEWQV.G
Retrocopy SVKLLPLNDS<RYALYDATYETEESKKEDLVFISWGPESAPLKSSMIYASSKDAIKKKFTGIKHEWQVSG

Parental  LDDIKDLCFLEKSLKWNIVLRSESPP
          LDDIKD...L...L....V...E..P
Retrocopy LDDIKDRSTLGEKLGGSAVVSLEGKP

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	1.49 RPM	38.36 RPM
SRP017611_kidney	0.41 RPM	11.35 RPM
SRP017611_liver	0.31 RPM	7.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1397 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1397 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017048	7 retrocopies	retro_dnov_1072, retro_dnov_1379, retro_dnov_1697, retro_dnov_2195, retro_dnov_2691, retro_dnov_715, retro_dnov_905,
Erinaceus europaeus	ENSEEUG00000013155	4 retrocopies	retro_eeur_335, retro_eeur_448, retro_eeur_513, retro_eeur_578,
Echinops telfairi	ENSETEG00000006010	3 retrocopies	retro_etel_1579, retro_etel_1622, retro_etel_684,
Latimeria chalumnae	ENSLACG00000018011	1 retrocopy	retro_lcha_23,
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,
Monodelphis domestica	ENSMODG00000012949	1 retrocopy	retro_mdom_171,
Oryctolagus cuniculus	ENSOCUG00000009383	1 retrocopy	retro_ocun_1397 ,
Oryctolagus cuniculus	ENSOCUG00000025604	4 retrocopies	retro_ocun_1123, retro_ocun_1390, retro_ocun_324, retro_ocun_478,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891,
Sarcophilus harrisii	ENSSHAG00000004732	1 retrocopy	retro_shar_528,
Tupaia belangeri	ENSTBEG00000000391	2 retrocopies	retro_tbel_29, retro_tbel_4131,