RetrogeneDB ID: retro_itri_1177

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393394.1:1890911..1891880(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSSTOG00000013979
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_itri_1177
CAACGCTCCGCCCCCACTTCTGCCGCCACCAAACTGTGCGCCAACCCCCCACTGCCTACAGCTCCGCCACTATGGAGGAC
ACAAACAAGTACAGCAACATAGAAGAATTCGCAGAGGGATCCAAGAATCGAGAGCAAGAATCAGCAGGATGACGGTAAAA
TGTTTATTGGCAGCTTGAGCTGGGATAAGAGCAAGAAAGATCTGACTGAATATTTGTCTCAATTTGGGGAAGTTGTAGAC
TGTAGGATTAAAACAGATCCAGTCACTGGAAGATCAAGAGGATTTAGATTTGTGCTTTTTAAAGATGCTTGTAGTGTTGA
TAAGGTTTTGGAACTGAAAGAACACAAACTGGAGGGCAAATTGATAGACCCCTAAAGGGCCAAAGCTTTGAAATGGAAAG
AACCCCCTAAAAAGGTTTTTGTGGGTGGATTGAACCCAGATACTTCTGAAGAACAAATTAAAGAATATTTTGGAGCCTTT
GAAGAGATTGAAAATATTGAACTTCCCATGGATACAAAAACAAACCAAAGAAGAGGATTTTGCTTTATCACATATACAGA
TGAAGAGCCAGTAAAGAAATTGTTAGAAAGCAGATAACATCAAATTGGTTCTGGGAAATGTGAAATCAAAGTTGCACAGC
CCAAAGAGGTGTATAGGCAGCTACAGCAACAACAAAAAGGAGGAAGAGGTGCTGCAGCTGGTGGGTGAGGTGTACCAAGG
GTCGTGGCCGAGGTCAGGGCCAAAATGGAACCAAGGATTTAGTAACTATGATGATCAAGGATATGGAAATTACAATAGTG
CCTATGGTGGTGATGAGCACTATAGTGGCTATGGTGGATATGATTATACTGGGTATAACTATGGGAACTATGGGTATGGA
CAGAAATATGCAGACTACAGTGATCAACAGACACTTATGGCAAGGCTTCTCAAGGGGGTGGCAATCACCAAAATAATTAC
CAGCCATAC

Alignment

ORF - retro_itri_1177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.06 %
• Parental protein coverage: 77.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QRSAAAAAGTR-TARQHPTADSSATMEDMNEYSNIEEFAEGSK-INASKNQQDDGKMFIGGLSWDTSKKD
          QRSA...A.T..T.RQ.PTA.SSATMED.N.YSNIEEFAEGSK.I.....Q.DDGKMFIG.LSWD.SKKD
Retrocopy QRSAPTSAATK<TVRQPPTAYSSATMEDTNKYSNIEEFAEGSK>IESKNQQ-DDGKMFIGSLSWDKSKKD

Parental  LTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKEPPK
          LTEYLS.FGEVVDC.IKTDPVTGRSRGF.FVLFKDA.SVDKVLELKEHKL.GKLIDP.RAKALK.KEPPK
Retrocopy LTEYLSQFGEVVDCRIKTDPVTGRSRGFRFVLFKDACSVDKVLELKEHKLEGKLIDP*RAKALKWKEPPK

Parental  KVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGSGKC
          KVFVGGL.PDTSEEQIKEYFGAF.EIENIELPMDTKTN.RRGFCFITYTDEEPVKKLLESR.HQIGSGKC
Retrocopy KVFVGGLNPDTSEEQIKEYFGAFEEIENIELPMDTKTNQRRGFCFITYTDEEPVKKLLESR*HQIGSGKC

Parental  EIKVAQPKEVYRQQQQQQKGGRGAAAGGRG-GTRGRGRGQGQN-WNQGFNNYYDQGYGNYNSAYGGDQNY
          EIKVAQPKEVYRQ.QQQQKGGRGAAAGG.G..T.GRGRGQGQN.WNQGF.NY.DQGYGNYNSAYGGD..Y
Retrocopy EIKVAQPKEVYRQLQQQQKGGRGAAAGG*G<CTKGRGRGQGQN<WNQGFSNYDDQGYGNYNSAYGGDEHY

Parental  SGYGGYDYTGYNYGNYGYGQGYADYSGQQS-TYGKASRGGGNHQNNYQPY
          SGYGGYDYTGYNYGNYGYGQ.YADYS.QQ..TYGKAS.GGGNHQNNYQPY
Retrocopy SGYGGYDYTGYNYGNYGYGQKYADYSDQQT<TYGKASQGGGNHQNNYQPY

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_1177 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1177 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 13 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015197	1 retrocopy	retro_cjac_2589,
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Felis catus	ENSFCAG00000000455	1 retrocopy	retro_fcat_1568,
Macropus eugenii	ENSMEUG00000011454	7 retrocopies	retro_meug_1252, retro_meug_1378, retro_meug_1491, retro_meug_1971, retro_meug_2165, retro_meug_249, retro_meug_766,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Sarcophilus harrisii	ENSSHAG00000013616	3 retrocopies	retro_shar_297, retro_shar_527, retro_shar_625,
Ictidomys tridecemlineatus	ENSSTOG00000006202	3 retrocopies	retro_itri_1723, retro_itri_448, retro_itri_717,
Ictidomys tridecemlineatus	ENSSTOG00000006551	8 retrocopies	retro_itri_1291, retro_itri_1567, retro_itri_190, retro_itri_354, retro_itri_439, retro_itri_446, retro_itri_456, retro_itri_515,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177 ,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Tupaia belangeri	ENSTBEG00000002817	7 retrocopies	retro_tbel_2079, retro_tbel_2283, retro_tbel_2608, retro_tbel_2874, retro_tbel_3344, retro_tbel_4302, retro_tbel_4405,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,