RetrogeneDB ID: retro_itri_1480

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393502.1:48770..49292(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL12A
• Ensembl ID: ENSSTOG00000027658
• Aliases: None
• Description: myosin, light chain 12A, regulatory, non-sarcomeric [Source:HGNC Symbol;Acc:16701]

Sequence

>retro_itri_1480
ATGTCGAGCAAAAGAGCAAAGACCAAGACCACCAAGAAGTGCCCTCAATGCACAACATGTACATCCAATGTGTTTGTCAT
GTTTGACCAATCACAGATTCAGGAATTCAAGAGGCCTTCAACATAATTGACCAGAACAGAGATGGTTTCATTGACAAGGA
AGATTTGCATGATATGCTTGCCTCACTGGGGAAGAATCCCACTGATGAATACCTGGATGTCATGATGAATGAGGCTCCAG
GACCCATCAATTTCACCGTGTTCCTCACCATGTTTGGTGAGAAATTAAATGACTCAGATCCCAAAGATGTTAATAGAAAT
ACATTTGCTTGCTTTGATGAAGAAGCTACTGGCACCATTCAGGAGGATTACCTGAGAGAGTTGCTGACCATTCATGGGCG
ATTGGTTTACAGATAAGGAAGTGGATGAGCTGTACAGAGAAGCCCCTATTGACAGATAGGGGAATTTCAATTACATCAAG
TTCGTGTACATTCTTAAACACGTAGCAAAAGACAAAGATGAC

Alignment

ORF - retro_itri_1480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSSKRAKTKTTKKRPQ--RATSNVFAMFDQSQIQEFK-EAFNMIDQNRDGFIDKEDLHDMLASLGKNPTD
          MSSKRAKTKTTKK.PQ....TSNVF.MFDQSQIQEFK.EAFN.IDQNRDGFIDKEDLHDMLASLGKNPTD
Retrocopy MSSKRAKTKTTKKCPQCTTCTSNVFVMFDQSQIQEFK<EAFNIIDQNRDGFIDKEDLHDMLASLGKNPTD

Parental  EYLDAMMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTT-MGDRFTD
          EYLD.MMNEAPGPINFT.FLTMFGEKLN..DP.DV.RN.FACFDEEATGTIQEDYLRELLT..MGD.FTD
Retrocopy EYLDVMMNEAPGPINFTVFLTMFGEKLNDSDPKDVNRNTFACFDEEATGTIQEDYLRELLTI>MGDWFTD

Parental  EEVDELYREAPIDKKGNFNYIEFTRILKHGAKDKDD
          .EVDELYREAPID..GNFNYI.F..ILKH.AKDKDD
Retrocopy KEVDELYREAPIDR*GNFNYIKFVYILKHVAKDKDD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1480 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1480 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016024	2 retrocopies	retro_btau_1273, retro_btau_1693,
Canis familiaris	ENSCAFG00000029134	3 retrocopies	retro_cfam_166, retro_cfam_583, retro_cfam_79,
Choloepus hoffmanni	ENSCHOG00000005206	54 retrocopies	retro_chof_1002, retro_chof_1149, retro_chof_1238, retro_chof_1250, retro_chof_1273, retro_chof_1321, retro_chof_1326, retro_chof_135, retro_chof_1352, retro_chof_1363, retro_chof_1374, retro_chof_1439, retro_chof_1505, retro_chof_1520, retro_chof_1538, retro_chof_1553, retro_chof_1574, retro_chof_1594, retro_chof_1608, retro_chof_1641, retro_chof_1694, retro_chof_1783, retro_chof_1790, retro_chof_1798, retro_chof_1801, retro_chof_1804, retro_chof_1809, retro_chof_1875, retro_chof_1879, retro_chof_1887, retro_chof_2059, retro_chof_2114, retro_chof_2157, retro_chof_2180, retro_chof_2353, retro_chof_2430, retro_chof_2492, retro_chof_2510, retro_chof_2516, retro_chof_2597, retro_chof_2638, retro_chof_2639, retro_chof_2689, retro_chof_543, retro_chof_545, retro_chof_584, retro_chof_606, retro_chof_618, retro_chof_667, retro_chof_686, retro_chof_696, retro_chof_729, retro_chof_752, retro_chof_949,
Callithrix jacchus	ENSCJAG00000038151	2 retrocopies	retro_cjac_1279, retro_cjac_3119,
Echinops telfairi	ENSETEG00000011271	3 retrocopies	retro_etel_393, retro_etel_439, retro_etel_96,
Microcebus murinus	ENSMICG00000017884	2 retrocopies	retro_mmur_1194, retro_mmur_1585,
Mus musculus	ENSMUSG00000024048	1 retrocopy	retro_mmus_1149,
Otolemur garnettii	ENSOGAG00000001340	7 retrocopies	retro_ogar_1877, retro_ogar_2516, retro_ogar_2536, retro_ogar_2540, retro_ogar_347, retro_ogar_517, retro_ogar_605,
Sorex araneus	ENSSARG00000011512	1 retrocopy	retro_sara_102,
Ictidomys tridecemlineatus	ENSSTOG00000027658	2 retrocopies	retro_itri_1480 , retro_itri_896,