RetrogeneDB ID: retro_ocun_900

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:7980068..7980598(+)
• Located in intron of: ENSOCUG00000012015

Retrocopy information

• Ensembl ID: ENSOCUG00000014619
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MYL12B
• Ensembl ID: ENSOCUG00000021304
• Aliases: None
• Description: myosin, light chain 12B, regulatory [Source:HGNC Symbol;Acc:29827]

Sequence

>retro_ocun_900
GACTTAACCACCACCATGTCGGGCAAAAGGGCAAAGACCAAGACCACCAAGAAGCGCCCTCAGCGTGCCACGTCCAGTGT
GTTTGCCATGTTTGGCCAGTCACAGATTCAGGAGTTCAAAGAGGCCTTCAACATGATTGATCAGAACCGAGGCGGTTTCA
TTGACAAGGAGGATTTGCACGATATGCTTGCTTCACTGGGGAAAAATCCAACTGATGAGTATCTGGACGCCATGATGAGT
GAGGCTCCAGGCCCCATCAGTTTCACCATGTTTCTCACCGTGTTTGGTAAGAAGTTGAATGGCACAGATCCAGAAGATGT
CATCAGAAATGCTTTTGCTTGCTTTGATGAAGAAGAACTGGCACCATTCAGGAGGACTACCTGAGAGAGCTGCTGACAAC
CATGGGAGACCGGTTTACAGACGAGGAGGTGGACGAGCTCTACAGAGAAGCTCCCATTGACAAAAAGGGGAACTTCAATT
ACATTGGGTTCACACGCATCCTTAAACATGGAGCAAAAGACAAGGATGAC

Alignment

ORF - retro_ocun_900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.26 %
• Parental protein coverage: 99.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLTTTMSSKRAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNP
          DLTTTMS.KRAKTKTTKKRPQRATS.VFAMF.QSQIQEFKEAFNMIDQNR.GFIDKEDLHDMLASLGKNP
Retrocopy DLTTTMSGKRAKTKTTKKRPQRATSSVFAMFGQSQIQEFKEAFNMIDQNRGGFIDKEDLHDMLASLGKNP

Parental  TDAYLDAMMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEE-ATGTIQEDYLRELLTTMGDRF
          TD.YLDAMM.EAPGPI.FTMFLT.FG.KLNGTDPEDVIRNAFACFDEE..TGTIQEDYLRELLTTMGDRF
Retrocopy TDEYLDAMMSEAPGPISFTMFLTVFGKKLNGTDPEDVIRNAFACFDEE<RTGTIQEDYLRELLTTMGDRF

Parental  TDEEVDELYREAPIDKKGNFNYIEFTRILKHGAKDKDD
          TDEEVDELYREAPIDKKGNFNYI.FTRILKHGAKDKDD
Retrocopy TDEEVDELYREAPIDKKGNFNYIGFTRILKHGAKDKDD

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	9.22 RPM	73.46 RPM
SRP017611_kidney	30.71 RPM	120.41 RPM
SRP017611_liver	4.86 RPM	37.61 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_900 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_900 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_900 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000006985	1 retrocopy	retro_eeur_311,
Gorilla gorilla	ENSGGOG00000004051	4 retrocopies	retro_ggor_1139, retro_ggor_1140, retro_ggor_2330, retro_ggor_2675,
Oryctolagus cuniculus	ENSOCUG00000021304	1 retrocopy	retro_ocun_900 ,
Rattus norvegicus	ENSRNOG00000015733	2 retrocopies	retro_rnor_1614, retro_rnor_2718,
Tupaia belangeri	ENSTBEG00000009299	4 retrocopies	retro_tbel_1294, retro_tbel_1629, retro_tbel_3088, retro_tbel_3438,
Tarsius syrichta	ENSTSYG00000010418	9 retrocopies	retro_tsyr_1034, retro_tsyr_1265, retro_tsyr_1320, retro_tsyr_1464, retro_tsyr_1961, retro_tsyr_2054, retro_tsyr_277, retro_tsyr_391, retro_tsyr_751,