RetrogeneDB ID: retro_itri_1598

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393564.1:126744..127188(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024440
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EAPP
• Ensembl ID: ENSSTOG00000005273
• Aliases: None
• Description: E2F-associated phosphoprotein [Source:HGNC Symbol;Acc:19312]

Sequence

>retro_itri_1598
CTATATGATCCTGAAAAAGATAACAGAGACCAGGCCTGGGTTGATGCACAGAGAAGGGGTTATCATGGTTTTGGGTTACA
GAGGCCACGTCATCAACAGCCTGTTCCAAATAGTGATGCTGTTTTGAATTGCCCAGCTTGCATGACGACACTGTGCCTTG
ATTGCCAAAGGCATGAATCCTACAAAACTCAATATAGAGCAATGTTCGTGATGAATTGTTCTGTCAACAAAGAGGAGGTT
CTAAGATATAAAAACTCAGAGAACAGGAAGAAAAGGCGGGGCTATAAGAAGATGAAGTCTAACCATGAAGACTCTGCAGA
GCAGGCAGAGACAGAAGTGGAAGAAATCTATCACCCAGTCATGTGTACAGAATGTTCCACAGAAGTGGCAGTCTACGACA
AGGATGAAGTCTTTCATTTTTTCAATGTTTTAGCAAGCCATTCC

Alignment

ORF - retro_itri_1598 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.54 %
• Parental protein coverage: 51.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFIPYRTNRSLIYVDSYRHNXHGFGLQRPRHQQPVPNSDAVLNCPACMTTLCLDCQRHESYKTQYRAMFV
          L..P...NR....VD..R...HGFGLQRPRHQQPVPNSDAVLNCPACMTTLCLDCQRHESYKTQYRAMFV
Retrocopy LYDPEKDNRDQAWVDAQRRGYHGFGLQRPRHQQPVPNSDAVLNCPACMTTLCLDCQRHESYKTQYRAMFV

Parental  MNCSVNKEEVLRYKNSENRKKRRGYKKMKSNHEDSAEQAETEVEEIYHPVMCTECSTEVAVYDKDEVFHF
          MNCSVNKEEVLRYKNSENRKKRRGYKKMKSNHEDSAEQAETEVEEIYHPVMCTECSTEVAVYDKDEVFHF
Retrocopy MNCSVNKEEVLRYKNSENRKKRRGYKKMKSNHEDSAEQAETEVEEIYHPVMCTECSTEVAVYDKDEVFHF

Parental  FNVLASHS
          FNVLASHS
Retrocopy FNVLASHS

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_1598 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1598 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005391	1 retrocopy	retro_cjac_3231,
Cavia porcellus	ENSCPOG00000003005	1 retrocopy	retro_cpor_898,
Myotis lucifugus	ENSMLUG00000013814	1 retrocopy	retro_mluc_596,
Monodelphis domestica	ENSMODG00000014525	1 retrocopy	retro_mdom_1226,
Mustela putorius furo	ENSMPUG00000001029	1 retrocopy	retro_mputfur_19,
Oryctolagus cuniculus	ENSOCUG00000003226	1 retrocopy	retro_ocun_1701,
Ictidomys tridecemlineatus	ENSSTOG00000005273	2 retrocopies	retro_itri_1598 , retro_itri_237,
Tupaia belangeri	ENSTBEG00000001306	1 retrocopy	retro_tbel_4258,