RetrogeneDB ID: retro_itri_1470

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393499.1:1509159..1509728(-)
• Located in intron of: ENSSTOG00000026038

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMA1
• Ensembl ID: ENSSTOG00000006270
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, alpha type, 1 [Source:HGNC Symbol;Acc:9530]

Sequence

>retro_itri_1470
ATGACAATGAAGTCACTGTTTGGCAGAGTTTATCCAACTGAATATGCAACGGAAGCTGTTAAACAAGGTTCAGCCACAGT
TGGTCTGAAATCGAAATTGCATGCAGAGATGGCTGCATTGAAAAGAGTATAGTCCGAATTTGCTGCTCACCAGGAAAAAT
TCTCCACGCTGACAACCATATTGGTATCTCAACTTGGGGGTTTACTGCTGATGCTAGACTGTTATGTAATTTTATGTTCC
ATGAGTTGTTTGGAAATCAGACTTTATTTGACAAGACCACTCCCTGGGTCTCATCTTGCACCTCTAACTAGAAGCAAGAC
CCGGATACCAACACAGTGGTACGGCTGGAGACCATATGGTGTCAGCTGCTTGCTGCTGGCTATGGTGATATGAGCACTCA
CATTTTCCAAACCTACCCGCCTGCCATTAACTATTTTGACTGCAGAGTTCTGTCCATGTGAGCCCTTTCTCCATCAATTC
ACACTTCCTCAAAGAGACATATGTCTGAGTTTATGGAATGGAACTCAAATGAACAGGTTAAACATGGACTCTGTACCTTC
AATGAGACA

Alignment

ORF - retro_itri_1470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.77 %
• Parental protein coverage: 72.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQK-KILHVDNHIGISIAGLT
          .T..S..GR....EYA.EAVKQGSATVGLKSK.HA...ALKR..SE.AAHQ..KILH.DNHIGIS..G.T
Retrocopy MTMKSLFGRVYPTEYATEAVKQGSATVGLKSKLHAEMAALKRV*SEFAAHQE<KILHADNHIGISTWGFT

Parental  ADARLLCNFMRQE-CLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVG-LLIAGYDDMGPHIFQ
          ADARLLCNFM..E.CL..R....RPLP.S.L..L..SKT.IPTQ.YG.RPYGV..LL.AGY.DM..HIFQ
Retrocopy ADARLLCNFMFHE>CLEIRLYLTRPLPGSHLAPLTRSKTRIPTQWYGWRPYGVS<LLAAGYGDMSTHIFQ

Parental  TCPSA-NYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRET
          T.P.A.NYFDCR..S..A.S.S..T...RHMSEFME.N.NE.VKHGL....ET
Retrocopy TYPPAINYFDCRVLSM*ALSPSIHTSSKRHMSEFMEWNSNEQVKHGLCTFNET

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_1470 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1470 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 23 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002440	2 retrocopies	retro_amel_1733, retro_amel_1903,
Bos taurus	ENSBTAG00000006564	1 retrocopy	retro_btau_1833,
Choloepus hoffmanni	ENSCHOG00000005395	11 retrocopies	retro_chof_155, retro_chof_1844, retro_chof_1991, retro_chof_2376, retro_chof_2626, retro_chof_267, retro_chof_2712, retro_chof_459, retro_chof_519, retro_chof_719, retro_chof_77,
Equus caballus	ENSECAG00000024086	1 retrocopy	retro_ecab_1078,
Felis catus	ENSFCAG00000011381	1 retrocopy	retro_fcat_972,
Homo sapiens	ENSG00000129084	1 retrocopy	retro_hsap_4720,
Gorilla gorilla	ENSGGOG00000001416	1 retrocopy	retro_ggor_2933,
Macropus eugenii	ENSMEUG00000011112	1 retrocopy	retro_meug_71,
Myotis lucifugus	ENSMLUG00000009251	4 retrocopies	retro_mluc_2444, retro_mluc_2445, retro_mluc_2463, retro_mluc_2515,
Macaca mulatta	ENSMMUG00000016446	1 retrocopy	retro_mmul_2509,
Mustela putorius furo	ENSMPUG00000013199	4 retrocopies	retro_mputfur_1243, retro_mputfur_224, retro_mputfur_338, retro_mputfur_825,
Mus musculus	ENSMUSG00000030751	1 retrocopy	retro_mmus_831,
Nomascus leucogenys	ENSNLEG00000017705	1 retrocopy	retro_nleu_1990,
Oryctolagus cuniculus	ENSOCUG00000000439	2 retrocopies	retro_ocun_1461, retro_ocun_1490,
Otolemur garnettii	ENSOGAG00000011622	3 retrocopies	retro_ogar_2267, retro_ogar_2644, retro_ogar_992,
Ochotona princeps	ENSOPRG00000013677	1 retrocopy	retro_opri_370,
Pongo abelii	ENSPPYG00000003466	2 retrocopies	retro_pabe_1883, retro_pabe_3664,
Pan troglodytes	ENSPTRG00000003385	1 retrocopy	retro_ptro_3137,
Sarcophilus harrisii	ENSSHAG00000015626	1 retrocopy	retro_shar_217,
Ictidomys tridecemlineatus	ENSSTOG00000006270	2 retrocopies	retro_itri_1470 , retro_itri_987,
Tupaia belangeri	ENSTBEG00000012037	3 retrocopies	retro_tbel_2629, retro_tbel_323, retro_tbel_982,
Tarsius syrichta	ENSTSYG00000003869	2 retrocopies	retro_tsyr_1723, retro_tsyr_374,
Vicugna pacos	ENSVPAG00000008820	3 retrocopies	retro_vpac_344, retro_vpac_648, retro_vpac_82,